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- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Nanoplot: long reads\"];\n 0 -->|output| 3;\n 73d0e4cf-366e-41c1-810a-b269638826b3[\"Output\\nNanoPlot on input dataset(s): HTML report\"];\n 3 --> 73d0e4cf-366e-41c1-810a-b269638826b3;\n style 73d0e4cf-366e-41c1-810a-b269638826b3 stroke:#2c3143,stroke-width:4px;\n 4[\"FastQC on R1\"];\n 1 -->|output| 4;\n 5[\"FastQC on R2\"];\n 2 -->|output| 5;\n 6[\"MultiQC: combine fastQC reports\"];\n 4 -->|text_file| 6;\n 5 -->|text_file| 6;\n 8baf8700-876e-4a74-ad99-6e656f3ba618[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n 6 --> 8baf8700-876e-4a74-ad99-6e656f3ba618;\n style 8baf8700-876e-4a74-ad99-6e656f3ba618 stroke:#2c3143,stroke-width:4px;",
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- "name": "Data QC - upgraded",
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- "license": "GPL-3.0-or-later",
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Minimap2 round 1: map reads to assembly\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 3[\"Racon round 1: polish assembly\"];\n 0 -->|output| 3;\n 2 -->|alignment_output| 3;\n 1 -->|output| 3;\n 4[\"Minimap2 round 2: map reads to assembly\"];\n 1 -->|output| 4;\n 3 -->|consensus| 4;\n 5[\"Racon round 2: polish assembly\"];\n 3 -->|consensus| 5;\n 4 -->|alignment_output| 5;\n 1 -->|output| 5;\n 594819c3-668e-4575-b9a6-4459ffacf952[\"Output\\nAssembly polished by short reads using Racon\"];\n 5 --> 594819c3-668e-4575-b9a6-4459ffacf952;\n style 594819c3-668e-4575-b9a6-4459ffacf952 stroke:#2c3143,stroke-width:4px;",
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- "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
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- "name": "Racon polish with long reads, x4 - upgraded",
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9def2c6e-fd3c-4969-b5d4-d13c187c1144 stroke:#2c3143,stroke-width:4px;\n 61f7a150-a4a2-46b1-89f5-2170d466656e[\"Output\\nGenome annotation statistics: summary (second round)\"];\n 14 --> 61f7a150-a4a2-46b1-89f5-2170d466656e;\n style 61f7a150-a4a2-46b1-89f5-2170d466656e stroke:#2c3143,stroke-width:4px;\n 15[\"Train SNAP\"];\n 2 -->|output| 15;\n 11 -->|output_gff| 15;\n 458887f7-0661-4bde-ab1a-875aac6caed8[\"Output\\nSNAP: trained model\"];\n 15 --> 458887f7-0661-4bde-ab1a-875aac6caed8;\n style 458887f7-0661-4bde-ab1a-875aac6caed8 stroke:#2c3143,stroke-width:4px;\n 16[\"Busco\"];\n 12 -->|output_exons| 16;\n f52b1b41-0ea5-4384-bd43-4927273c909c[\"Output\\nBusco summary second round\"];\n 16 --> f52b1b41-0ea5-4384-bd43-4927273c909c;\n style f52b1b41-0ea5-4384-bd43-4927273c909c stroke:#2c3143,stroke-width:4px;\n 17[\"Maker\"];\n 13 -->|output_tar| 17;\n 15 -->|output| 17;\n 2 -->|output| 17;\n 11 -->|output_full| 17;\n 18[\"Map annotation ids\"];\n 17 -->|output_gff| 18;\n 63575dcf-54d1-4cb1-b5fb-a2810b4da807[\"Output\\nMap annotation ids: renamed GFF\"];\n 18 --> 63575dcf-54d1-4cb1-b5fb-a2810b4da807;\n style 63575dcf-54d1-4cb1-b5fb-a2810b4da807 stroke:#2c3143,stroke-width:4px;\n 19[\"JBrowse\"];\n 2 -->|output| 19;\n 3 -->|output_gff| 19;\n 18 -->|renamed| 19;\n 11 -->|output_gff| 19;\n 3 -->|output_evidences| 19;\n 11 -->|output_evidences| 19;\n 17 -->|output_evidences| 19;\n 5a38ae83-e177-45f3-aa9f-4c1844584fa5[\"Output\\nJBrowse: report\"];\n 19 --> 5a38ae83-e177-45f3-aa9f-4c1844584fa5;\n style 5a38ae83-e177-45f3-aa9f-4c1844584fa5 stroke:#2c3143,stroke-width:4px;\n 20[\"gffread\"];\n 18 -->|renamed| 20;\n 2 -->|output| 20;\n 52fcac23-b612-4377-a19a-2e3b667a23e3[\"Output\\nGffread: exons\"];\n 20 --> 52fcac23-b612-4377-a19a-2e3b667a23e3;\n style 52fcac23-b612-4377-a19a-2e3b667a23e3 stroke:#2c3143,stroke-width:4px;\n 5c47c25e-0ddb-4ade-a5d0-873ff4add28c[\"Output\\nGffread: translation of cds\"];\n 20 --> 5c47c25e-0ddb-4ade-a5d0-873ff4add28c;\n style 5c47c25e-0ddb-4ade-a5d0-873ff4add28c stroke:#2c3143,stroke-width:4px;\n 84d9183b-9589-464b-9f82-4dae7f87133e[\"Output\\nGffread: cds\"];\n 20 --> 84d9183b-9589-464b-9f82-4dae7f87133e;\n style 84d9183b-9589-464b-9f82-4dae7f87133e stroke:#2c3143,stroke-width:4px;\n 21[\"Genome annotation statistics\"];\n 18 -->|renamed| 21;\n 2 -->|output| 21;\n f5d4a6bf-1ff8-435a-8084-7921e25bff3a[\"Output\\nGenome annotation statistics: graphs (third round)\"];\n 21 --> f5d4a6bf-1ff8-435a-8084-7921e25bff3a;\n style f5d4a6bf-1ff8-435a-8084-7921e25bff3a stroke:#2c3143,stroke-width:4px;\n 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42[\"Output\\nGenome annotation statistics: summary (third round)\"];\n 21 --> 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42;\n style 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42 stroke:#2c3143,stroke-width:4px;\n 22[\"Busco\"];\n 20 -->|output_exons| 22;\n 0bc78676-eecc-4168-894d-34c4ca07cdf3[\"Output\\nBusco summary final round\"];\n 22 --> 0bc78676-eecc-4168-894d-34c4ca07cdf3;\n style 0bc78676-eecc-4168-894d-34c4ca07cdf3 stroke:#2c3143,stroke-width:4px;",
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- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nsamples_profile\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nreference_genome_of_tested_strain\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Convert compressed file to uncompressed.\"];\n 2 -->|output| 3;\n 9d6bde4a-7180-4097-9ffd-6992111a617c[\"Output\\ndecompressed_rg_file\"];\n 3 --> 9d6bde4a-7180-4097-9ffd-6992111a617c;\n style 9d6bde4a-7180-4097-9ffd-6992111a617c stroke:#2c3143,stroke-width:4px;\n 4[\"Map with minimap2\"];\n 1 -->|output| 4;\n 0 -->|output| 4;\n 3 -->|output1| 4;\n 31779c23-4f26-418e-9418-2551e883dbe7[\"Output\\nmap_with_minimap2\"];\n 4 --> 31779c23-4f26-418e-9418-2551e883dbe7;\n style 31779c23-4f26-418e-9418-2551e883dbe7 stroke:#2c3143,stroke-width:4px;\n 5[\"Clair3\"];\n 4 -->|alignment_output| 5;\n 3 -->|output1| 5;\n 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53[\"Output\\nclair3_pileup_vcf\"];\n 5 --> 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53;\n style 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53 stroke:#2c3143,stroke-width:4px;\n 987f9145-83ab-44f1-801a-b0d527ecbce8[\"Output\\nclair3_full_alignment_vcf\"];\n 5 --> 987f9145-83ab-44f1-801a-b0d527ecbce8;\n style 987f9145-83ab-44f1-801a-b0d527ecbce8 stroke:#2c3143,stroke-width:4px;\n fab82215-f59a-43b1-92d7-37629a1fdb65[\"Output\\nclair3_merged_output\"];\n 5 --> fab82215-f59a-43b1-92d7-37629a1fdb65;\n style fab82215-f59a-43b1-92d7-37629a1fdb65 stroke:#2c3143,stroke-width:4px;\n 6[\"Samtools depth\"];\n 4 -->|alignment_output| 6;\n 7[\"Samtools coverage\"];\n 4 -->|alignment_output| 7;\n 8[\"bcftools norm\"];\n 5 -->|merge_output| 8;\n 3 -->|output1| 8;\n 22553aa1-f5db-4d37-87c4-1164dbb3d2d5[\"Output\\nnormalized_vcf_output\"];\n 8 --> 22553aa1-f5db-4d37-87c4-1164dbb3d2d5;\n style 22553aa1-f5db-4d37-87c4-1164dbb3d2d5 stroke:#2c3143,stroke-width:4px;\n 9[\"Advanced Cut\"];\n 6 -->|output| 9;\n 10[\"Remove beginning\"];\n 7 -->|output| 10;\n 11[\"SnpSift Filter\"];\n 8 -->|output_file| 11;\n 3e7981ec-2205-4571-93eb-10c0dd14b288[\"Output\\nquality_filtered_vcf_output\"];\n 11 --> 3e7981ec-2205-4571-93eb-10c0dd14b288;\n style 3e7981ec-2205-4571-93eb-10c0dd14b288 stroke:#2c3143,stroke-width:4px;\n 12[\"Table Compute\"];\n 9 -->|output| 12;\n 13[\"Cut\"];\n 10 -->|out_file1| 13;\n 14[\"SnpSift Extract Fields\"];\n 11 -->|output| 14;\n 1b0f4f2c-4717-45be-b580-fe10cba78c35[\"Output\\nextracted_fields_from_the_vcf_output\"];\n 14 --> 1b0f4f2c-4717-45be-b580-fe10cba78c35;\n style 1b0f4f2c-4717-45be-b580-fe10cba78c35 stroke:#2c3143,stroke-width:4px;\n 15[\"bcftools consensus\"];\n 11 -->|output| 15;\n 3 -->|output1| 15;\n 49497f3c-9332-4924-bcfd-cb71788ad2c2[\"Output\\nbcftools_consensus\"];\n 15 --> 49497f3c-9332-4924-bcfd-cb71788ad2c2;\n style 49497f3c-9332-4924-bcfd-cb71788ad2c2 stroke:#2c3143,stroke-width:4px;\n 16[\"Select first\"];\n 13 -->|out_file1| 16;\n 17[\"Remove beginning\"];\n 14 -->|output| 17;\n 18[\"Collapse Collection\"];\n 16 -->|outfile| 18;\n 5ee1c158-1a85-45ca-9abd-b30632b3092c[\"Output\\nmapping_coverage_percentage_per_sample\"];\n 18 --> 5ee1c158-1a85-45ca-9abd-b30632b3092c;\n style 5ee1c158-1a85-45ca-9abd-b30632b3092c stroke:#2c3143,stroke-width:4px;\n 19[\"Count\"];\n 17 -->|out_file1| 19;\n 20[\"Advanced Cut\"];\n 18 -->|output| 20;\n 21[\"Cut\"];\n 19 -->|out_file1| 21;\n 22[\"Paste\"];\n 20 -->|output| 22;\n 12 -->|table| 22;\n 25b7b87b-5ef1-487f-90cc-81351a2f81ce[\"Output\\nmapping_mean_depth_per_sample\"];\n 22 --> 25b7b87b-5ef1-487f-90cc-81351a2f81ce;\n style 25b7b87b-5ef1-487f-90cc-81351a2f81ce stroke:#2c3143,stroke-width:4px;\n 23[\"Select first\"];\n 21 -->|out_file1| 23;\n 24[\"Collapse Collection\"];\n 23 -->|outfile| 24;\n 25[\"Column Regex Find And Replace\"];\n 24 -->|output| 25;\n 2852c4ee-24ea-4df7-b59e-54eb6e2f470b[\"Output\\nnumber_of_variants_per_sample\"];\n 25 --> 2852c4ee-24ea-4df7-b59e-54eb6e2f470b;\n style 2852c4ee-24ea-4df7-b59e-54eb6e2f470b stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-06-24 00:06:32 +0000",
- "name": "Allele-based Pathogen Identification",
- "path": "topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/allele_based_pathogen_identification.ga",
- "test_results": null,
- "tests": true,
- "title": "Allele-based Pathogen Identification",
- "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-pathogen-detection-from-nanopore-foodborne-data/versions/allele_based_pathogen_identification",
- "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/allele_based_pathogen_identification.ga",
- "wfid": "microbiome-pathogen-detection-from-nanopore-foodborne-data",
- "wfname": "allele_based_pathogen_identification",
- "workflow": "allele_based_pathogen_identification.ga"
- },
- {
- "creators": [
- {
- "class": "Person",
- "identifier": "0000-0001-9047-4215",
- "name": "Engy Nasr",
- "url": "https://orcid.org/0000-0001-9047-4215"
- },
- {
- "class": "Person",
- "identifier": "0000-0001-9852-1987",
- "name": "B\u00e9r\u00e9nice Batut",
- "url": "https://orcid.org/0000-0001-9852-1987"
- },
- {
- "class": "Person",
- "identifier": "0000-0003-2982-388X",
- "name": "Paul Zierep"
- }
- ],
- "license": "MIT",
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Extract element identifiers\"];\n 0 -->|output| 1;\n d82a93c6-23a9-4f85-879c-ecd759a31087[\"Output\\nextracted_samples_IDs\"];\n 1 --> d82a93c6-23a9-4f85-879c-ecd759a31087;\n style d82a93c6-23a9-4f85-879c-ecd759a31087 stroke:#2c3143,stroke-width:4px;\n 2[\"Build list\"];\n 0 -->|output| 2;\n f5b5b256-8ddf-4da8-8111-b1f6d3025a0d[\"Output\\nlist_of_lists_of_preprocessed_samples\"];\n 2 --> f5b5b256-8ddf-4da8-8111-b1f6d3025a0d;\n style f5b5b256-8ddf-4da8-8111-b1f6d3025a0d stroke:#2c3143,stroke-width:4px;\n 3[\"Split file\"];\n 1 -->|output| 3;\n eb5317bd-4bad-4cad-9219-3ac379221d6e[\"Output\\nsplitted_extracted_samples_IDs\"];\n 3 --> eb5317bd-4bad-4cad-9219-3ac379221d6e;\n style eb5317bd-4bad-4cad-9219-3ac379221d6e stroke:#2c3143,stroke-width:4px;\n 4[\"Flye\"];\n 2 -->|output| 4;\n ff0d8c7b-2ac7-4c6d-a110-f71418dad938[\"Output\\nflye_consensus_fasta\"];\n 4 --> ff0d8c7b-2ac7-4c6d-a110-f71418dad938;\n style ff0d8c7b-2ac7-4c6d-a110-f71418dad938 stroke:#2c3143,stroke-width:4px;\n 2385436f-fbe8-4d77-a40b-27a097d02941[\"Output\\nflye_assembly_graph\"];\n 4 --> 2385436f-fbe8-4d77-a40b-27a097d02941;\n style 2385436f-fbe8-4d77-a40b-27a097d02941 stroke:#2c3143,stroke-width:4px;\n 0e42ce51-c46b-45d8-baa4-45c0e98ac712[\"Output\\nflye_assembly_gfa\"];\n 4 --> 0e42ce51-c46b-45d8-baa4-45c0e98ac712;\n style 0e42ce51-c46b-45d8-baa4-45c0e98ac712 stroke:#2c3143,stroke-width:4px;\n 3f297aed-7cee-4999-bbf4-69d84de6b64f[\"Output\\nflye_assembly_info_tabular\"];\n 4 --> 3f297aed-7cee-4999-bbf4-69d84de6b64f;\n style 3f297aed-7cee-4999-bbf4-69d84de6b64f stroke:#2c3143,stroke-width:4px;\n 5[\"Parse parameter value\"];\n 3 -->|list_output_txt| 5;\n 3608e170-c462-42a2-8003-f3f65baa3834[\"Output\\nparsed_extracted_samples_IDs_to_text\"];\n 5 --> 3608e170-c462-42a2-8003-f3f65baa3834;\n style 3608e170-c462-42a2-8003-f3f65baa3834 stroke:#2c3143,stroke-width:4px;\n 6[\"medaka consensus pipeline\"];\n 4 -->|consensus| 6;\n 0 -->|output| 6;\n 9e5ad6ec-b408-4132-ba07-dec9fa626923[\"Output\\nmedaka_gaps_in_draft_bed_file\"];\n 6 --> 9e5ad6ec-b408-4132-ba07-dec9fa626923;\n style 9e5ad6ec-b408-4132-ba07-dec9fa626923 stroke:#2c3143,stroke-width:4px;\n fcbd3e3f-2e93-4798-b696-dad7db9f2efd[\"Output\\nmedaka_log_file\"];\n 6 --> fcbd3e3f-2e93-4798-b696-dad7db9f2efd;\n style fcbd3e3f-2e93-4798-b696-dad7db9f2efd stroke:#2c3143,stroke-width:4px;\n 60656aac-ad2a-4c9b-9a68-b9fb18ae5595[\"Output\\nmedaka_propability_h5_file\"];\n 6 --> 60656aac-ad2a-4c9b-9a68-b9fb18ae5595;\n style 60656aac-ad2a-4c9b-9a68-b9fb18ae5595 stroke:#2c3143,stroke-width:4px;\n c790d434-8e78-4df0-a0d4-8f9da0692158[\"Output\\nmedaka_calls_of_draft_bam_file\"];\n 6 --> c790d434-8e78-4df0-a0d4-8f9da0692158;\n style c790d434-8e78-4df0-a0d4-8f9da0692158 stroke:#2c3143,stroke-width:4px;\n df361e19-b6d1-405b-96cc-b48c1ab7c604[\"Output\\nsample_all_contigs\"];\n 6 --> df361e19-b6d1-405b-96cc-b48c1ab7c604;\n style df361e19-b6d1-405b-96cc-b48c1ab7c604 stroke:#2c3143,stroke-width:4px;\n 7[\"Bandage Image\"];\n 4 -->|assembly_gfa| 7;\n 9612a851-1f94-4d54-b001-5d082bcc9055[\"Output\\nbandage_assembly_graph_image\"];\n 7 --> 9612a851-1f94-4d54-b001-5d082bcc9055;\n style 9612a851-1f94-4d54-b001-5d082bcc9055 stroke:#2c3143,stroke-width:4px;\n 8[\"Compose text parameter value\"];\n 5 -->|text_param| 8;\n 9[\"FASTA-to-Tabular\"];\n 6 -->|out_consensus| 9;\n de06c362-5b0a-4c29-956e-fbf02539789a[\"Output\\nsample_specific_contigs_tabular_file_preparation\"];\n 9 --> de06c362-5b0a-4c29-956e-fbf02539789a;\n style de06c362-5b0a-4c29-956e-fbf02539789a stroke:#2c3143,stroke-width:4px;\n 10[\"ABRicate\"];\n 6 -->|out_consensus| 10;\n 8f227fc7-2d92-4c6f-af64-e841c1315b4f[\"Output\\nabricate_with_vfdb_to_identify_genes_with_VFs\"];\n 10 --> 8f227fc7-2d92-4c6f-af64-e841c1315b4f;\n style 8f227fc7-2d92-4c6f-af64-e841c1315b4f stroke:#2c3143,stroke-width:4px;\n 11[\"ABRicate\"];\n 6 -->|out_consensus| 11;\n fa021d98-d885-4834-ac62-f30d5792260e[\"Output\\nabricate_report_using_ncbi_database_to_indentify_amr\"];\n 11 --> fa021d98-d885-4834-ac62-f30d5792260e;\n style fa021d98-d885-4834-ac62-f30d5792260e stroke:#2c3143,stroke-width:4px;\n 12[\"Replace\"];\n 8 -->|out1| 12;\n 9 -->|output| 12;\n 174cb2c3-ed28-453c-8afb-85150e0b51ad[\"Output\\nsample_specific_contigs_tabular_file\"];\n 12 --> 174cb2c3-ed28-453c-8afb-85150e0b51ad;\n style 174cb2c3-ed28-453c-8afb-85150e0b51ad stroke:#2c3143,stroke-width:4px;\n 13[\"Replace\"];\n 8 -->|out1| 13;\n 10 -->|report| 13;\n 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad[\"Output\\nvfs\"];\n 13 --> 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad;\n style 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad stroke:#2c3143,stroke-width:4px;\n 14[\"Replace\"];\n 8 -->|out1| 14;\n 11 -->|report| 14;\n a8eb74a5-362b-4f0f-a944-672e27981a41[\"Output\\namrs\"];\n 14 --> a8eb74a5-362b-4f0f-a944-672e27981a41;\n style a8eb74a5-362b-4f0f-a944-672e27981a41 stroke:#2c3143,stroke-width:4px;\n 15[\"Tabular-to-FASTA\"];\n 12 -->|outfile| 15;\n a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe[\"Output\\ncontigs\"];\n 15 --> a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe;\n style a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-06-24 00:06:32 +0000",
- "name": "Gene-based Pathogen Identification",
- "path": "topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/gene_based_pathogen_identification.ga",
- "test_results": null,
- "tests": true,
- "title": "Gene-based Pathogen Identification",
- "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-pathogen-detection-from-nanopore-foodborne-data/versions/gene_based_pathogen_identification",
- "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/gene_based_pathogen_identification.ga",
- "wfid": "microbiome-pathogen-detection-from-nanopore-foodborne-data",
- "wfname": "gene_based_pathogen_identification",
- "workflow": "gene_based_pathogen_identification.ga"
- },
- {
- "creators": [
- {
- "class": "Person",
- "identifier": "0000-0001-9852-1987",
- "name": "B\u00e9r\u00e9nice Batut",
- "url": "https://orcid.org/0000-0001-9852-1987"
- },
- {
- "class": "Person",
- "identifier": "0000-0001-9047-4215",
- "name": "Engy Nasr",
- "url": "https://orcid.org/0000-0001-9047-4215"
- },
- {
- "class": "Person",
- "identifier": "0000-0003-2982-388X",
- "name": "Paul Zierep"
- }
- ],
- "license": "MIT",
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Parameter\\nsamples_profile\"];\n style 0 fill:#ded,stroke:#393,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\ncollection_of_all_samples\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Porechop\"];\n 1 -->|output| 2;\n 34ea26db-11cb-41ee-85c3-75af8a53a2c0[\"Output\\nporechop_output_trimmed_reads\"];\n 2 --> 34ea26db-11cb-41ee-85c3-75af8a53a2c0;\n style 34ea26db-11cb-41ee-85c3-75af8a53a2c0 stroke:#2c3143,stroke-width:4px;\n 3[\"NanoPlot\"];\n 1 -->|output| 3;\n 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd[\"Output\\nnanoplot_qc_on_reads_before_preprocessing_nanostats\"];\n 3 --> 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd;\n style 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd stroke:#2c3143,stroke-width:4px;\n 304110f9-60d0-4ba2-8b3b-fae0e2a49554[\"Output\\nnanoplot_on_reads_before_preprocessing_nanostats_post_filtering\"];\n 3 --> 304110f9-60d0-4ba2-8b3b-fae0e2a49554;\n style 304110f9-60d0-4ba2-8b3b-fae0e2a49554 stroke:#2c3143,stroke-width:4px;\n f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e[\"Output\\nnanoplot_qc_on_reads_before_preprocessing_html_report\"];\n 3 --> f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e;\n style f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e stroke:#2c3143,stroke-width:4px;\n 4[\"FastQC\"];\n 1 -->|output| 4;\n d0a64624-05d0-4068-835b-a025fc011760[\"Output\\nfastqc_quality_check_before_preprocessing_html_file\"];\n 4 --> d0a64624-05d0-4068-835b-a025fc011760;\n style d0a64624-05d0-4068-835b-a025fc011760 stroke:#2c3143,stroke-width:4px;\n e61fef5d-1bc8-4c8e-be6a-f74e210e9920[\"Output\\nfastqc_quality_check_before_preprocessing_text_file\"];\n 4 --> e61fef5d-1bc8-4c8e-be6a-f74e210e9920;\n style e61fef5d-1bc8-4c8e-be6a-f74e210e9920 stroke:#2c3143,stroke-width:4px;\n 5[\"fastp\"];\n 2 -->|outfile| 5;\n a2219483-50b7-4aed-98dd-333ad2e12eb8[\"Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal\"];\n 5 --> a2219483-50b7-4aed-98dd-333ad2e12eb8;\n style a2219483-50b7-4aed-98dd-333ad2e12eb8 stroke:#2c3143,stroke-width:4px;\n 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4[\"Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report\"];\n 5 --> 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4;\n style 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4 stroke:#2c3143,stroke-width:4px;\n 6[\"MultiQC\"];\n 4 -->|text_file| 6;\n ebffe782-a56c-431f-8af4-c0cb8d7a02fc[\"Output\\nmultiQC_stats_before_preprocessing\"];\n 6 --> ebffe782-a56c-431f-8af4-c0cb8d7a02fc;\n style ebffe782-a56c-431f-8af4-c0cb8d7a02fc stroke:#2c3143,stroke-width:4px;\n 0f92196d-047d-4918-819d-c0ff7cd3ae85[\"Output\\nmultiQC_html_report_before_preprocessing\"];\n 6 --> 0f92196d-047d-4918-819d-c0ff7cd3ae85;\n style 0f92196d-047d-4918-819d-c0ff7cd3ae85 stroke:#2c3143,stroke-width:4px;\n 7[\"Map with minimap2\"];\n 0 -->|output| 7;\n 5 -->|out1| 7;\n 9d7bb3b7-09a1-401f-a132-bb35a53375ea[\"Output\\nbam_map_to_host\"];\n 7 --> 9d7bb3b7-09a1-401f-a132-bb35a53375ea;\n style 9d7bb3b7-09a1-401f-a132-bb35a53375ea stroke:#2c3143,stroke-width:4px;\n 8[\"NanoPlot\"];\n 5 -->|out1| 8;\n b5899290-4c57-4662-ad22-860654652ade[\"Output\\nnanoplot_qc_on_reads_after_preprocessing_html_report\"];\n 8 --> b5899290-4c57-4662-ad22-860654652ade;\n style b5899290-4c57-4662-ad22-860654652ade stroke:#2c3143,stroke-width:4px;\n 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf[\"Output\\nnanoplot_on_reads_after_preprocessing_nanostats_post_filtering\"];\n 8 --> 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf;\n style 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf stroke:#2c3143,stroke-width:4px;\n 42db7f93-919e-4bbb-81a1-06411a9da410[\"Output\\nnanoplot_qc_on_reads_after_preprocessing_nanostats\"];\n 8 --> 42db7f93-919e-4bbb-81a1-06411a9da410;\n style 42db7f93-919e-4bbb-81a1-06411a9da410 stroke:#2c3143,stroke-width:4px;\n 9[\"FastQC\"];\n 5 -->|out1| 9;\n 09306471-afa0-4106-9cc7-259b93dfc862[\"Output\\nfastqc_quality_check_after_preprocessing_text_file\"];\n 9 --> 09306471-afa0-4106-9cc7-259b93dfc862;\n style 09306471-afa0-4106-9cc7-259b93dfc862 stroke:#2c3143,stroke-width:4px;\n 084f982f-20f1-457e-8012-91ebbb85633d[\"Output\\nfastqc_quality_check_after_preprocessing_html_file\"];\n 9 --> 084f982f-20f1-457e-8012-91ebbb85633d;\n style 084f982f-20f1-457e-8012-91ebbb85633d stroke:#2c3143,stroke-width:4px;\n 10[\"Split BAM by reads mapping status\"];\n 7 -->|alignment_output| 10;\n 14a53fe2-f296-43aa-86b7-243278c1050c[\"Output\\nnon_host_sequences_bam\"];\n 10 --> 14a53fe2-f296-43aa-86b7-243278c1050c;\n style 14a53fe2-f296-43aa-86b7-243278c1050c stroke:#2c3143,stroke-width:4px;\n 3b1e626f-6bc1-484c-be01-366534361b73[\"Output\\nhost_sequences_bam\"];\n 10 --> 3b1e626f-6bc1-484c-be01-366534361b73;\n style 3b1e626f-6bc1-484c-be01-366534361b73 stroke:#2c3143,stroke-width:4px;\n 11[\"Select\"];\n 9 -->|text_file| 11;\n a809853b-119f-44d2-986b-8d2006439fbe[\"Output\\ntotal_sequences_before_hosts_sequences_removal\"];\n 11 --> a809853b-119f-44d2-986b-8d2006439fbe;\n style a809853b-119f-44d2-986b-8d2006439fbe stroke:#2c3143,stroke-width:4px;\n 12[\"Samtools fastx\"];\n 10 -->|mapped| 12;\n 10d4eaec-81d8-444e-8075-7b77a1fb6870[\"Output\\nhost_sequences_fastq\"];\n 12 --> 10d4eaec-81d8-444e-8075-7b77a1fb6870;\n style 10d4eaec-81d8-444e-8075-7b77a1fb6870 stroke:#2c3143,stroke-width:4px;\n 13[\"Samtools fastx\"];\n 10 -->|unmapped| 13;\n 0c2dd74d-ac4f-45cf-839c-50386a7ece28[\"Output\\nnon_host_sequences_fastq\"];\n 13 --> 0c2dd74d-ac4f-45cf-839c-50386a7ece28;\n style 0c2dd74d-ac4f-45cf-839c-50386a7ece28 stroke:#2c3143,stroke-width:4px;\n 14[\"Collapse Collection\"];\n 11 -->|out_file1| 14;\n 15[\"Filter failed datasets\"];\n 12 -->|output| 15;\n 16[\"Kraken2\"];\n 13 -->|output| 16;\n 203d303e-8f3a-4242-971f-b345842ebdb8[\"Output\\nkraken2_with_kalamri_database_output\"];\n 16 --> 203d303e-8f3a-4242-971f-b345842ebdb8;\n style 203d303e-8f3a-4242-971f-b345842ebdb8 stroke:#2c3143,stroke-width:4px;\n 843afd4d-23a8-46e7-b945-8b67dd7ae341[\"Output\\nkraken2_with_kalamri_database_report\"];\n 16 --> 843afd4d-23a8-46e7-b945-8b67dd7ae341;\n style 843afd4d-23a8-46e7-b945-8b67dd7ae341 stroke:#2c3143,stroke-width:4px;\n 17[\"Cut\"];\n 14 -->|output| 17;\n d07be9f1-d250-4008-91ee-59a68521eb56[\"Output\\nquality_retained_all_reads\"];\n 17 --> d07be9f1-d250-4008-91ee-59a68521eb56;\n style d07be9f1-d250-4008-91ee-59a68521eb56 stroke:#2c3143,stroke-width:4px;\n 18[\"FastQC\"];\n 15 -->|output| 18;\n b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7[\"Output\\nhosts_qc_text_file\"];\n 18 --> b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7;\n style b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7 stroke:#2c3143,stroke-width:4px;\n b72ff57b-0921-43bf-a817-6cd444c8f3cb[\"Output\\nhosts_qc_html\"];\n 18 --> b72ff57b-0921-43bf-a817-6cd444c8f3cb;\n style b72ff57b-0921-43bf-a817-6cd444c8f3cb stroke:#2c3143,stroke-width:4px;\n 19[\"Krakentools: Extract Kraken Reads By ID\"];\n 5 -->|out1| 19;\n 16 -->|report_output| 19;\n 16 -->|output| 19;\n 57e3b725-8e13-40b2-9acc-31fd56ebc80a[\"Output\\ncollection_of_preprocessed_samples\"];\n 19 --> 57e3b725-8e13-40b2-9acc-31fd56ebc80a;\n style 57e3b725-8e13-40b2-9acc-31fd56ebc80a stroke:#2c3143,stroke-width:4px;\n 20[\"Select\"];\n 18 -->|text_file| 20;\n 3ba35c71-32f0-4741-98d4-ea8522e27500[\"Output\\ntotal_sequences_after_hosts_sequences_removal\"];\n 20 --> 3ba35c71-32f0-4741-98d4-ea8522e27500;\n style 3ba35c71-32f0-4741-98d4-ea8522e27500 stroke:#2c3143,stroke-width:4px;\n 21[\"Collapse Collection\"];\n 20 -->|out_file1| 21;\n 22[\"Cut\"];\n 21 -->|output| 22;\n cef36c68-4549-4fd6-b7c8-71fb21df012f[\"Output\\nquality_retained_hosts_reads\"];\n 22 --> cef36c68-4549-4fd6-b7c8-71fb21df012f;\n style cef36c68-4549-4fd6-b7c8-71fb21df012f stroke:#2c3143,stroke-width:4px;\n 23[\"Column join\"];\n 17 -->|out_file1| 23;\n 22 -->|out_file1| 23;\n 24[\"Compute\"];\n 23 -->|tabular_output| 24;\n 25[\"Column Regex Find And Replace\"];\n 24 -->|out_file1| 25;\n 470892ee-dab9-48d7-ad97-45dbd52afaa7[\"Output\\nremoved_hosts_percentage_tabular\"];\n 25 --> 470892ee-dab9-48d7-ad97-45dbd52afaa7;\n style 470892ee-dab9-48d7-ad97-45dbd52afaa7 stroke:#2c3143,stroke-width:4px;\n 26[\"MultiQC\"];\n 9 -->|text_file| 26;\n 25 -->|out_file1| 26;\n 0b1b5a73-36ee-42a2-a220-1ced6ec7378b[\"Output\\nmultiQC_html_report_after_preprocessing\"];\n 26 --> 0b1b5a73-36ee-42a2-a220-1ced6ec7378b;\n style 0b1b5a73-36ee-42a2-a220-1ced6ec7378b stroke:#2c3143,stroke-width:4px;\n 13cbf6c7-6954-4458-aa66-a5b020c63822[\"Output\\nmultiQC_stats_after_preprocessing\"];\n 26 --> 13cbf6c7-6954-4458-aa66-a5b020c63822;\n style 13cbf6c7-6954-4458-aa66-a5b020c63822 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-06-24 00:06:32 +0000",
- "name": "Nanopore Preprocessing",
- "path": "topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/nanopore_preprocessing.ga",
- "test_results": null,
- "tests": true,
- "title": "Nanopore Preprocessing",
- "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-pathogen-detection-from-nanopore-foodborne-data/versions/nanopore_preprocessing",
- "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/nanopore_preprocessing.ga",
- "wfid": "microbiome-pathogen-detection-from-nanopore-foodborne-data",
- "wfname": "nanopore_preprocessing",
- "workflow": "nanopore_preprocessing.ga"
- },
- {
- "creators": [
- {
- "class": "Person",
- "identifier": "0000-0001-9047-4215",
- "name": "Engy Nasr",
- "url": "https://orcid.org/0000-0001-9047-4215"
- },
- {
- "class": "Person",
- "identifier": "0000-0001-9852-1987",
- "name": "B\u00e9r\u00e9nice Batut",
- "url": "https://orcid.org/0000-0001-9852-1987"
- },
- {
- "class": "Person",
- "identifier": "0000-0003-2982-388X",
- "name": "Paul Zierep"
- }
- ],
- "license": "MIT",
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\namr_identified_by_ncbi\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nvfs_of_genes_identified_by_vfdb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nmetadata\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nremoved_hosts_percentage_tabular\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nmapping_mean_depth_per_sample\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Collection\\namrs\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nmapping_coverage_percentage_per_sample\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"\u2139\ufe0f Input Dataset\\nnumber_of_variants_per_sample\"];\n style 7 stroke:#2c3143,stroke-width:4px;\n 8[\"\u2139\ufe0f Input Collection\\ncontigs\"];\n style 8 stroke:#2c3143,stroke-width:4px;\n 9[\"\u2139\ufe0f Input Collection\\nvfs\"];\n style 9 stroke:#2c3143,stroke-width:4px;\n 10[\"Filter failed datasets\"];\n 0 -->|output| 10;\n 11[\"Filter failed datasets\"];\n 1 -->|output| 11;\n 12[\"Bar chart\"];\n 3 -->|output| 12;\n 0961166e-38b6-44e3-93db-100d821b0070[\"Output\\nnumber_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig\"];\n 12 --> 0961166e-38b6-44e3-93db-100d821b0070;\n style 0961166e-38b6-44e3-93db-100d821b0070 stroke:#2c3143,stroke-width:4px;\n 13[\"Bar chart\"];\n 3 -->|output| 13;\n 548975e5-4619-49fc-9e95-4d7f4d761dfd[\"Output\\nremoved_host_percentage_fig\"];\n 13 --> 548975e5-4619-49fc-9e95-4d7f4d761dfd;\n style 548975e5-4619-49fc-9e95-4d7f4d761dfd stroke:#2c3143,stroke-width:4px;\n 14[\"Bar chart\"];\n 4 -->|output| 14;\n a71ebb67-1154-4f25-a62d-e8fa2b839e2e[\"Output\\nmapping_mean_depth_per_sample_fig\"];\n 14 --> a71ebb67-1154-4f25-a62d-e8fa2b839e2e;\n style a71ebb67-1154-4f25-a62d-e8fa2b839e2e stroke:#2c3143,stroke-width:4px;\n 15[\"Filter failed datasets\"];\n 5 -->|output| 15;\n 16[\"Bar chart\"];\n 6 -->|output| 16;\n 2567360e-d39f-4316-84f5-77aaf8e8198c[\"Output\\nmapping_coverage_percentage_per_sample_fig\"];\n 16 --> 2567360e-d39f-4316-84f5-77aaf8e8198c;\n style 2567360e-d39f-4316-84f5-77aaf8e8198c stroke:#2c3143,stroke-width:4px;\n 17[\"Bar chart\"];\n 7 -->|output| 17;\n 68c76f06-d2ea-4280-9e6f-a7b4f1568389[\"Output\\nnumber_of_Variants_and_SNPs_indentified_fig\"];\n 17 --> 68c76f06-d2ea-4280-9e6f-a7b4f1568389;\n style 68c76f06-d2ea-4280-9e6f-a7b4f1568389 stroke:#2c3143,stroke-width:4px;\n 18[\"Filter failed datasets\"];\n 8 -->|output| 18;\n 19[\"Filter failed datasets\"];\n 9 -->|output| 19;\n 20[\"Remove beginning\"];\n 10 -->|output| 20;\n 21[\"Remove beginning\"];\n 11 -->|output| 21;\n 22[\"Remove beginning\"];\n 15 -->|output| 22;\n 23[\"Collapse Collection\"];\n 18 -->|output| 23;\n 86910e39-57bf-4a76-ac4c-739340fd2387[\"Output\\nall_samples_contigs_in_one_fasta_file\"];\n 23 --> 86910e39-57bf-4a76-ac4c-739340fd2387;\n style 86910e39-57bf-4a76-ac4c-739340fd2387 stroke:#2c3143,stroke-width:4px;\n 24[\"Collapse Collection\"];\n 19 -->|output| 24;\n 02b996c6-a912-4e4e-b3ec-49601faaa452[\"Output\\nall_vfs_in_one_tabular\"];\n 24 --> 02b996c6-a912-4e4e-b3ec-49601faaa452;\n style 02b996c6-a912-4e4e-b3ec-49601faaa452 stroke:#2c3143,stroke-width:4px;\n 25[\"Remove beginning\"];\n 19 -->|output| 25;\n 26[\"Count\"];\n 20 -->|out_file1| 26;\n 27[\"Count\"];\n 21 -->|out_file1| 27;\n 28[\"Group\"];\n 21 -->|out_file1| 28;\n 29[\"Unique\"];\n 22 -->|out_file1| 29;\n 30[\"Split by group\"];\n 24 -->|output| 30;\n 59f8cb09-424b-47b1-b94b-a612c2610cab[\"Output\\nsplit_by_group_collection\"];\n 30 --> 59f8cb09-424b-47b1-b94b-a612c2610cab;\n style 59f8cb09-424b-47b1-b94b-a612c2610cab stroke:#2c3143,stroke-width:4px;\n 31[\"Unique\"];\n 25 -->|out_file1| 31;\n 32[\"Cut\"];\n 26 -->|out_file1| 32;\n 33[\"Cut\"];\n 27 -->|out_file1| 33;\n 34[\"Filter empty datasets\"];\n 28 -->|out_file1| 34;\n 35[\"Cut\"];\n 29 -->|outfile| 35;\n 36[\"Cut\"];\n 30 -->|split_output| 36;\n eeb25a51-ea21-4a19-a196-55d5bd919b10[\"Output\\nadjusted_abricate_vfs_tabular_part1\"];\n 36 --> eeb25a51-ea21-4a19-a196-55d5bd919b10;\n style eeb25a51-ea21-4a19-a196-55d5bd919b10 stroke:#2c3143,stroke-width:4px;\n 37[\"Cut\"];\n 31 -->|outfile| 37;\n 38[\"Collapse Collection\"];\n 32 -->|out_file1| 38;\n 39[\"Collapse Collection\"];\n 33 -->|out_file1| 39;\n 40[\"Column join\"];\n 34 -->|output| 40;\n 41[\"bedtools getfasta\"];\n 23 -->|output| 41;\n 35 -->|out_file1| 41;\n 42[\"Remove beginning\"];\n 36 -->|out_file1| 42;\n aaaa4446-0817-4e5c-aa1b-9ec384f2a363[\"Output\\nadjusted_abricate_vfs_tabular_part2\"];\n 42 --> aaaa4446-0817-4e5c-aa1b-9ec384f2a363;\n style aaaa4446-0817-4e5c-aa1b-9ec384f2a363 stroke:#2c3143,stroke-width:4px;\n 43[\"bedtools getfasta\"];\n 23 -->|output| 43;\n 37 -->|out_file1| 43;\n 44[\"Column Regex Find And Replace\"];\n 38 -->|output| 44;\n 4809c36b-31ef-4664-8e4e-47f0f72152de[\"Output\\namrs_count\"];\n 44 --> 4809c36b-31ef-4664-8e4e-47f0f72152de;\n style 4809c36b-31ef-4664-8e4e-47f0f72152de stroke:#2c3143,stroke-width:4px;\n 45[\"Column Regex Find And Replace\"];\n 39 -->|output| 45;\n 87efc81d-4d84-4af3-831f-dfe033c59f78[\"Output\\nvfs_count\"];\n 45 --> 87efc81d-4d84-4af3-831f-dfe033c59f78;\n style 87efc81d-4d84-4af3-831f-dfe033c59f78 stroke:#2c3143,stroke-width:4px;\n 46[\"Column Regex Find And Replace\"];\n 40 -->|tabular_output| 46;\n f5c221e3-00ef-4834-9a5f-a94c97fd6764[\"Output\\nheatmap_table\"];\n 46 --> f5c221e3-00ef-4834-9a5f-a94c97fd6764;\n style f5c221e3-00ef-4834-9a5f-a94c97fd6764 stroke:#2c3143,stroke-width:4px;\n 47[\"Regex Find And Replace\"];\n 41 -->|output| 47;\n 48[\"bedtools getfasta\"];\n 23 -->|output| 48;\n 42 -->|out_file1| 48;\n 82ce2107-89a3-438c-95bb-dc871b5258b7[\"Output\\nfiltered_sequences_with_vfs_fasta\"];\n 48 --> 82ce2107-89a3-438c-95bb-dc871b5258b7;\n style 82ce2107-89a3-438c-95bb-dc871b5258b7 stroke:#2c3143,stroke-width:4px;\n 49[\"Regex Find And Replace\"];\n 43 -->|output| 49;\n 50[\"Multi-Join\"];\n 45 -->|out_file1| 50;\n 44 -->|out_file1| 50;\n 51[\"Heatmap w ggplot\"];\n 46 -->|out_file1| 51;\n c0417c91-a513-4c6a-9a62-3aac2f1f8e85[\"Output\\nheatmap_pdf\"];\n 51 --> c0417c91-a513-4c6a-9a62-3aac2f1f8e85;\n style c0417c91-a513-4c6a-9a62-3aac2f1f8e85 stroke:#2c3143,stroke-width:4px;\n 97816bc2-fd0c-4077-a721-8dd1470879d1[\"Output\\nheatmap_png\"];\n 51 --> 97816bc2-fd0c-4077-a721-8dd1470879d1;\n style 97816bc2-fd0c-4077-a721-8dd1470879d1 stroke:#2c3143,stroke-width:4px;\n 52[\"Filter empty datasets\"];\n 47 -->|out_file1| 52;\n 53[\"ClustalW\"];\n 48 -->|output| 53;\n 9b7bd78c-f112-480b-a7df-c10711af254c[\"Output\\nclustalw_on_input_dnd\"];\n 53 --> 9b7bd78c-f112-480b-a7df-c10711af254c;\n style 9b7bd78c-f112-480b-a7df-c10711af254c stroke:#2c3143,stroke-width:4px;\n 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- "stderr": "Path to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nIllumina\t2\tAGATCGGAAGAGC\t50000\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t50000\t0.00\nNextera\t0\tCTGTCTCTTATA\t50000\t0.00\nUsing Illumina adapter for trimming (count: 2). Second best hit was smallRNA (count: 0)\n\nWriting report to './input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.85 s (17 us/read; 3.52 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 50,000\nReads with adapters: 14,011 (28.0%)\nReads written (passing filters): 50,000 (100.0%)\n\nTotal basepairs processed: 2,550,000 bp\nQuality-trimmed: 34,012 bp (1.3%)\nTotal written (filtered): 2,495,795 bp (97.9%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14011 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 27.3%\n C: 33.3%\n G: 24.8%\n T: 14.6%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9379\t12500.0\t0\t9379\n2\t3646\t3125.0\t0\t3646\n3\t791\t781.2\t0\t791\n4\t134\t195.3\t0\t134\n5\t33\t48.8\t0\t33\n6\t9\t12.2\t0\t9\n7\t3\t3.1\t0\t3\n8\t1\t0.8\t0\t1\n9\t1\t0.2\t0\t0 1\n10\t3\t0.0\t1\t0 3\n11\t1\t0.0\t1\t1\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t0 1\n19\t1\t0.0\t1\t1\n27\t1\t0.0\t1\t0 1\n28\t1\t0.0\t1\t0 1\n32\t1\t0.0\t1\t0 1\n36\t1\t0.0\t1\t0 1\n43\t1\t0.0\t1\t0 1\n49\t1\t0.0\t1\t0 1\n50\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to './input_2.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_2_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_2.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_2.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.91 s (18 us/read; 3.30 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 50,000\nReads with adapters: 13,787 (27.6%)\nReads written (passing filters): 50,000 (100.0%)\n\nTotal basepairs processed: 2,550,000 bp\nQuality-trimmed: 120,340 bp (4.7%)\nTotal written (filtered): 2,410,008 bp (94.5%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13787 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 27.6%\n C: 32.8%\n G: 24.6%\n T: 15.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9236\t12500.0\t0\t9236\n2\t3546\t3125.0\t0\t3546\n3\t827\t781.2\t0\t827\n4\t131\t195.3\t0\t131\n5\t36\t48.8\t0\t36\n6\t3\t12.2\t0\t3\n7\t2\t3.1\t0\t2\n9\t1\t0.2\t0\t0 1\n11\t2\t0.0\t1\t1 1\n15\t1\t0.0\t1\t1\n19\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\nfile_1: input_1_trimmed.fq.gz, file_2: input_2_trimmed.fq.gz\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq.gz and input_2_trimmed.fq.gz <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq.gz\nWriting validated paired-end read 2 reads to input_2_val_2.fq.gz\n\nTotal number of sequences analysed: 50000\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1639 (3.28%)\n\nDeleting both intermediate output files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\n\n====================================================================================================\n\n\ngzip: stdout: Broken pipe\n",
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Second best hit was smallRNA (count: 0)\n\nWriting report to './input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.85 s (17 us/read; 3.52 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 50,000\nReads with adapters: 14,011 (28.0%)\nReads written (passing filters): 50,000 (100.0%)\n\nTotal basepairs processed: 2,550,000 bp\nQuality-trimmed: 34,012 bp (1.3%)\nTotal written (filtered): 2,495,795 bp (97.9%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14011 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 27.3%\n C: 33.3%\n G: 24.8%\n T: 14.6%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9379\t12500.0\t0\t9379\n2\t3646\t3125.0\t0\t3646\n3\t791\t781.2\t0\t791\n4\t134\t195.3\t0\t134\n5\t33\t48.8\t0\t33\n6\t9\t12.2\t0\t9\n7\t3\t3.1\t0\t3\n8\t1\t0.8\t0\t1\n9\t1\t0.2\t0\t0 1\n10\t3\t0.0\t1\t0 3\n11\t1\t0.0\t1\t1\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t0 1\n19\t1\t0.0\t1\t1\n27\t1\t0.0\t1\t0 1\n28\t1\t0.0\t1\t0 1\n32\t1\t0.0\t1\t0 1\n36\t1\t0.0\t1\t0 1\n43\t1\t0.0\t1\t0 1\n49\t1\t0.0\t1\t0 1\n50\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to './input_2.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_2_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_2.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_2.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.91 s (18 us/read; 3.30 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 50,000\nReads with adapters: 13,787 (27.6%)\nReads written (passing filters): 50,000 (100.0%)\n\nTotal basepairs processed: 2,550,000 bp\nQuality-trimmed: 120,340 bp (4.7%)\nTotal written (filtered): 2,410,008 bp (94.5%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13787 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 27.6%\n C: 32.8%\n G: 24.6%\n T: 15.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9236\t12500.0\t0\t9236\n2\t3546\t3125.0\t0\t3546\n3\t827\t781.2\t0\t827\n4\t131\t195.3\t0\t131\n5\t36\t48.8\t0\t36\n6\t3\t12.2\t0\t3\n7\t2\t3.1\t0\t2\n9\t1\t0.2\t0\t0 1\n11\t2\t0.0\t1\t1 1\n15\t1\t0.0\t1\t1\n19\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\nfile_1: input_1_trimmed.fq.gz, file_2: input_2_trimmed.fq.gz\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq.gz and input_2_trimmed.fq.gz <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq.gz\nWriting validated paired-end read 2 reads to input_2_val_2.fq.gz\n\nTotal number of sequences analysed: 50000\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1639 (3.28%)\n\nDeleting both intermediate output files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\n\n====================================================================================================\n\n\ngzip: stdout: Broken pipe\n",
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batch - log\"];\n 6 --> 844f5e7c-78c8-4f28-8e15-cea35ada8fef;\n style 844f5e7c-78c8-4f28-8e15-cea35ada8fef stroke:#2c3143,stroke-width:4px;\n 7[\"Inspect AnnData\"];\n 0 -->|output| 7;\n 8[\"Plot\"];\n 0 -->|output| 8;\n 3b1232c5-d16a-434d-806e-79fd77f7c05f[\"Output\\nScatter - mito x UMIs\"];\n 8 --> 3b1232c5-d16a-434d-806e-79fd77f7c05f;\n style 3b1232c5-d16a-434d-806e-79fd77f7c05f stroke:#2c3143,stroke-width:4px;\n 9[\"Inspect AnnData\"];\n 0 -->|output| 9;\n 10[\"Plot\"];\n 0 -->|output| 10;\n a639cdc0-da40-4df9-8348-23117528b24a[\"Output\\nViolin - sex - log\"];\n 10 --> a639cdc0-da40-4df9-8348-23117528b24a;\n style a639cdc0-da40-4df9-8348-23117528b24a stroke:#2c3143,stroke-width:4px;\n 11[\"Plot\"];\n 2 -->|output_h5ad| 11;\n 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691[\"Output\\nViolin - Filterbygenes\"];\n 11 --> 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691;\n style 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691 stroke:#2c3143,stroke-width:4px;\n 12[\"Scanpy FilterCells\"];\n 2 -->|output_h5ad| 12;\n f378cb4e-0a77-49d9-b92a-752dbea4b09a[\"Output\\nCounts-filtered Object\"];\n 12 --> f378cb4e-0a77-49d9-b92a-752dbea4b09a;\n style f378cb4e-0a77-49d9-b92a-752dbea4b09a stroke:#2c3143,stroke-width:4px;\n 13[\"Inspect AnnData\"];\n 2 -->|output_h5ad| 13;\n f9e862db-eb22-4124-8fe0-0fdcfcfb8393[\"Output\\nGeneral - Filterbygenes\"];\n 13 --> f9e862db-eb22-4124-8fe0-0fdcfcfb8393;\n style f9e862db-eb22-4124-8fe0-0fdcfcfb8393 stroke:#2c3143,stroke-width:4px;\n 14[\"Inspect AnnData\"];\n 12 -->|output_h5ad| 14;\n 794f72b5-c2c3-46a0-ac15-b9f1e94941d2[\"Output\\nGeneral - Filterbycounts\"];\n 14 --> 794f72b5-c2c3-46a0-ac15-b9f1e94941d2;\n style 794f72b5-c2c3-46a0-ac15-b9f1e94941d2 stroke:#2c3143,stroke-width:4px;\n 15[\"Scanpy FilterCells\"];\n 12 -->|output_h5ad| 15;\n b915da66-6435-4871-baa0-3e494ba73c96[\"Output\\nMito-filtered Object\"];\n 15 --> b915da66-6435-4871-baa0-3e494ba73c96;\n style b915da66-6435-4871-baa0-3e494ba73c96 stroke:#2c3143,stroke-width:4px;\n 16[\"Plot\"];\n 12 -->|output_h5ad| 16;\n 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa[\"Output\\nViolin - Filterbycounts\"];\n 16 --> 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa;\n style 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa stroke:#2c3143,stroke-width:4px;\n 17[\"Inspect AnnData\"];\n 15 -->|output_h5ad| 17;\n cd94a4c6-5665-4bdf-88ea-4f4d41efa893[\"Output\\nGeneral - Filterbymito\"];\n 17 --> cd94a4c6-5665-4bdf-88ea-4f4d41efa893;\n style cd94a4c6-5665-4bdf-88ea-4f4d41efa893 stroke:#2c3143,stroke-width:4px;\n 18[\"Scanpy FilterGenes\"];\n 15 -->|output_h5ad| 18;\n ee63ef0a-98ed-45cb-b144-1154f84ae452[\"Output\\nFiltered Object\"];\n 18 --> ee63ef0a-98ed-45cb-b144-1154f84ae452;\n style ee63ef0a-98ed-45cb-b144-1154f84ae452 stroke:#2c3143,stroke-width:4px;\n 19[\"Plot\"];\n 15 -->|output_h5ad| 19;\n 7e48a14f-08fd-45ab-b613-606bf64dcf9d[\"Output\\nViolin - Filterbymito\"];\n 19 --> 7e48a14f-08fd-45ab-b613-606bf64dcf9d;\n style 7e48a14f-08fd-45ab-b613-606bf64dcf9d stroke:#2c3143,stroke-width:4px;\n 20[\"Inspect AnnData\"];\n 18 -->|output_h5ad| 20;\n d59efa9b-d049-4f0e-8bd8-8ae982a45d0a[\"Output\\nGeneral - Filtered object\"];\n 20 --> d59efa9b-d049-4f0e-8bd8-8ae982a45d0a;\n style d59efa9b-d049-4f0e-8bd8-8ae982a45d0a stroke:#2c3143,stroke-width:4px;\n 21[\"Scanpy NormaliseData\"];\n 18 -->|output_h5ad| 21;\n 22[\"Scanpy FindVariableGenes\"];\n 21 -->|output_h5ad| 22;\n 23[\"Scanpy ScaleData\"];\n 22 -->|output_h5ad| 23;\n 24[\"Scanpy RunPCA\"];\n 23 -->|output_h5ad| 24;\n 25[\"Plot\"];\n 24 -->|output_h5ad| 25;\n 993dea99-990f-460a-beb9-46e5c97ee898[\"Output\\nPCA Variance\"];\n 25 --> 993dea99-990f-460a-beb9-46e5c97ee898;\n style 993dea99-990f-460a-beb9-46e5c97ee898 stroke:#2c3143,stroke-width:4px;\n 26[\"Scanpy ComputeGraph\"];\n 24 -->|output_h5ad| 26;\n 27[\"Scanpy RunTSNE\"];\n 26 -->|output_h5ad| 27;\n 28[\"Scanpy RunUMAP\"];\n 27 -->|output_h5ad| 28;\n 29[\"Scanpy FindCluster\"];\n 28 -->|output_h5ad| 29;\n 30[\"Scanpy FindMarkers\"];\n 29 -->|output_h5ad| 30;\n 308b4961-4d50-442b-9bca-bbb1992426ba[\"Output\\nMarkers - cluster\"];\n 30 --> 308b4961-4d50-442b-9bca-bbb1992426ba;\n style 308b4961-4d50-442b-9bca-bbb1992426ba stroke:#2c3143,stroke-width:4px;\n 035bbbce-fb57-48c8-83d5-2b0cd0376541[\"Output\\nFinal object\"];\n 30 --> 035bbbce-fb57-48c8-83d5-2b0cd0376541;\n style 035bbbce-fb57-48c8-83d5-2b0cd0376541 stroke:#2c3143,stroke-width:4px;\n 31[\"Scanpy FindMarkers\"];\n 29 -->|output_h5ad| 31;\n 1705e219-192a-4f52-9b26-64fcbcd303ea[\"Output\\nMarkers - genotype\"];\n 31 --> 1705e219-192a-4f52-9b26-64fcbcd303ea;\n style 1705e219-192a-4f52-9b26-64fcbcd303ea stroke:#2c3143,stroke-width:4px;\n 32[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 32;\n 33[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 33;\n 34[\"Manipulate AnnData\"];\n 30 -->|output_h5ad| 34;\n 35[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 35;\n 36[\"Inspect AnnData\"];\n 30 -->|output_h5ad| 36;\n 37[\"AnnData Operations\"];\n 34 -->|anndata| 37;\n 30 -->|output_h5ad| 37;\n 38[\"Join two Datasets\"];\n 30 -->|output_tsv| 38;\n 36 -->|var| 38;\n 39[\"Join two Datasets\"];\n 31 -->|output_tsv| 39;\n 36 -->|var| 39;\n 40[\"AnnData Operations\"];\n 37 -->|output_h5ad| 40;\n a6d48df0-403f-4efc-a75f-9504a960884e[\"Output\\nFinal cell annotated object\"];\n 40 --> a6d48df0-403f-4efc-a75f-9504a960884e;\n style a6d48df0-403f-4efc-a75f-9504a960884e stroke:#2c3143,stroke-width:4px;\n 41[\"Cut\"];\n 38 -->|out_file1| 41;\n 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9[\"Output\\nMarkers - cluster - named\"];\n 41 --> 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9;\n style 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9 stroke:#2c3143,stroke-width:4px;\n 42[\"Cut\"];\n 39 -->|out_file1| 42;\n fdb88faa-9b76-4edb-b89b-427c098a473e[\"Output\\nMarkers - genotype - named\"];\n 42 --> fdb88faa-9b76-4edb-b89b-427c098a473e;\n style fdb88faa-9b76-4edb-b89b-427c098a473e stroke:#2c3143,stroke-width:4px;\n 43[\"Scanpy PlotEmbed\"];\n 40 -->|output_h5ad| 43;",
- "modified": "2024-06-24 00:06:33 +0000",
- "name": "CS3_Filter, Plot and Explore Single-cell RNA-seq Data",
- "path": "topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.ga",
- "test_results": null,
- "tests": false,
- "title": "CS3_Filter, Plot and Explore Single-cell RNA-seq Data",
- "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_basic-pipeline/versions/cs3_filter,_plot_and_explore_single-cell_rna-seq_data",
- "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.ga",
- "wfid": "single-cell-scrna-case_basic-pipeline",
- "wfname": "cs3_filter,_plot_and_explore_single-cell_rna-seq_data",
- "workflow": "CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.ga"
- },
- {
- "creators": [
- {
- "class": "Person",
- "identifier": "0000-0002-8170-8806",
- "name": "Wendi Bacon"
- },
- {
- "class": "Person",
- "identifier": "0009-0001-2017-8805",
- "name": "Julia Jakiela"
- }
- ],
- "license": "CC-BY-4.0",
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Inspect AnnData\"];\n 0 -->|output| 1;\n 2[\"Scanpy FilterCells\"];\n 0 -->|output| 2;\n 6a00b14b-d3f8-4771-963a-76115c8eaf2f[\"Output\\nGenes-filtered Object\"];\n 2 --> 6a00b14b-d3f8-4771-963a-76115c8eaf2f;\n style 6a00b14b-d3f8-4771-963a-76115c8eaf2f stroke:#2c3143,stroke-width:4px;\n 3[\"Plot\"];\n 0 -->|output| 3;\n c123842e-b2d2-43ad-81f0-6ba3b45d4021[\"Output\\nScatter - genes x UMIs\"];\n 3 --> c123842e-b2d2-43ad-81f0-6ba3b45d4021;\n style c123842e-b2d2-43ad-81f0-6ba3b45d4021 stroke:#2c3143,stroke-width:4px;\n 4[\"Plot\"];\n 0 -->|output| 4;\n f1020d4d-555e-42fa-ba21-52a151b91a5b[\"Output\\nScatter - mito x genes\"];\n 4 --> f1020d4d-555e-42fa-ba21-52a151b91a5b;\n style f1020d4d-555e-42fa-ba21-52a151b91a5b stroke:#2c3143,stroke-width:4px;\n 5[\"Plot\"];\n 0 -->|output| 5;\n a7fe6020-8f1e-470a-9ed3-f2b5e95516e0[\"Output\\nViolin - genotype - log\"];\n 5 --> a7fe6020-8f1e-470a-9ed3-f2b5e95516e0;\n style a7fe6020-8f1e-470a-9ed3-f2b5e95516e0 stroke:#2c3143,stroke-width:4px;\n 6[\"Plot\"];\n 0 -->|output| 6;\n 15e501bc-8ddb-4519-89eb-dde431ea96c1[\"Output\\nViolin - batch - log\"];\n 6 --> 15e501bc-8ddb-4519-89eb-dde431ea96c1;\n style 15e501bc-8ddb-4519-89eb-dde431ea96c1 stroke:#2c3143,stroke-width:4px;\n 7[\"Inspect AnnData\"];\n 0 -->|output| 7;\n 8[\"Plot\"];\n 0 -->|output| 8;\n eff22f46-baa6-4e00-ba82-d5e12ce26ff0[\"Output\\nScatter - mito x UMIs\"];\n 8 --> eff22f46-baa6-4e00-ba82-d5e12ce26ff0;\n style eff22f46-baa6-4e00-ba82-d5e12ce26ff0 stroke:#2c3143,stroke-width:4px;\n 9[\"Inspect AnnData\"];\n 0 -->|output| 9;\n 10[\"Plot\"];\n 0 -->|output| 10;\n 56677ca4-129c-476c-85ec-69d1bb3d800d[\"Output\\nViolin - sex - log\"];\n 10 --> 56677ca4-129c-476c-85ec-69d1bb3d800d;\n style 56677ca4-129c-476c-85ec-69d1bb3d800d stroke:#2c3143,stroke-width:4px;\n 11[\"Plot\"];\n 2 -->|output_h5ad| 11;\n acb61ea4-bcb9-45db-beef-e2bf1a176701[\"Output\\nViolin - Filterbygenes\"];\n 11 --> acb61ea4-bcb9-45db-beef-e2bf1a176701;\n style acb61ea4-bcb9-45db-beef-e2bf1a176701 stroke:#2c3143,stroke-width:4px;\n 12[\"Scanpy FilterCells\"];\n 2 -->|output_h5ad| 12;\n 51853662-4519-4229-a2ea-b22a53e7ef73[\"Output\\nCounts-filtered Object\"];\n 12 --> 51853662-4519-4229-a2ea-b22a53e7ef73;\n style 51853662-4519-4229-a2ea-b22a53e7ef73 stroke:#2c3143,stroke-width:4px;\n 13[\"Inspect AnnData\"];\n 2 -->|output_h5ad| 13;\n 362a7fe6-24bb-4398-ae48-870f4b4bb774[\"Output\\nGeneral - Filterbygenes\"];\n 13 --> 362a7fe6-24bb-4398-ae48-870f4b4bb774;\n style 362a7fe6-24bb-4398-ae48-870f4b4bb774 stroke:#2c3143,stroke-width:4px;\n 14[\"Inspect AnnData\"];\n 12 -->|output_h5ad| 14;\n edf24149-9341-4fe7-b10c-3fcf092faaa5[\"Output\\nGeneral - Filterbycounts\"];\n 14 --> edf24149-9341-4fe7-b10c-3fcf092faaa5;\n style edf24149-9341-4fe7-b10c-3fcf092faaa5 stroke:#2c3143,stroke-width:4px;\n 15[\"Scanpy FilterCells\"];\n 12 -->|output_h5ad| 15;\n a88ec405-265f-4a59-a75e-34e3b05b0096[\"Output\\nMito-filtered Object\"];\n 15 --> a88ec405-265f-4a59-a75e-34e3b05b0096;\n style a88ec405-265f-4a59-a75e-34e3b05b0096 stroke:#2c3143,stroke-width:4px;\n 16[\"Plot\"];\n 12 -->|output_h5ad| 16;\n a7c8b0d9-82d3-4438-a212-b5f7c56d36b8[\"Output\\nViolin - Filterbycounts\"];\n 16 --> a7c8b0d9-82d3-4438-a212-b5f7c56d36b8;\n style a7c8b0d9-82d3-4438-a212-b5f7c56d36b8 stroke:#2c3143,stroke-width:4px;\n 17[\"Inspect AnnData\"];\n 15 -->|output_h5ad| 17;\n 56882809-e19f-451a-8010-bc55dcee482f[\"Output\\nGeneral - Filterbymito\"];\n 17 --> 56882809-e19f-451a-8010-bc55dcee482f;\n style 56882809-e19f-451a-8010-bc55dcee482f stroke:#2c3143,stroke-width:4px;\n 18[\"Scanpy FilterGenes\"];\n 15 -->|output_h5ad| 18;\n 00846477-dec5-408a-83b2-105fff7ce05b[\"Output\\nFiltered Object\"];\n 18 --> 00846477-dec5-408a-83b2-105fff7ce05b;\n style 00846477-dec5-408a-83b2-105fff7ce05b stroke:#2c3143,stroke-width:4px;\n 19[\"Plot\"];\n 15 -->|output_h5ad| 19;\n 7582e113-2004-4255-a1f3-d3123373f342[\"Output\\nViolin - Filterbymito\"];\n 19 --> 7582e113-2004-4255-a1f3-d3123373f342;\n style 7582e113-2004-4255-a1f3-d3123373f342 stroke:#2c3143,stroke-width:4px;\n 20[\"Inspect AnnData\"];\n 18 -->|output_h5ad| 20;\n 2d870a40-c602-4a1c-afef-450489354d39[\"Output\\nGeneral - Filtered object\"];\n 20 --> 2d870a40-c602-4a1c-afef-450489354d39;\n style 2d870a40-c602-4a1c-afef-450489354d39 stroke:#2c3143,stroke-width:4px;\n 21[\"Scanpy NormaliseData\"];\n 18 -->|output_h5ad| 21;\n 22[\"Scanpy FindVariableGenes\"];\n 21 -->|output_h5ad| 22;\n a0eb92b1-0263-4179-b7af-4bd9bcc9c960[\"Output\\nUse_me_FVG\"];\n 22 --> a0eb92b1-0263-4179-b7af-4bd9bcc9c960;\n style a0eb92b1-0263-4179-b7af-4bd9bcc9c960 stroke:#2c3143,stroke-width:4px;\n 23[\"Scanpy ScaleData\"];\n 22 -->|output_h5ad| 23;\n 5776dbb9-0cac-40c0-9bae-9accae16a7a0[\"Output\\nUse_me_Scaled\"];\n 23 --> 5776dbb9-0cac-40c0-9bae-9accae16a7a0;\n style 5776dbb9-0cac-40c0-9bae-9accae16a7a0 stroke:#2c3143,stroke-width:4px;\n 24[\"Scanpy RunPCA\"];\n 23 -->|output_h5ad| 24;\n 25[\"Plot\"];\n 24 -->|output_h5ad| 25;\n f0b6f578-050f-4936-9ee7-9956b0760c6f[\"Output\\nPCA Variance\"];\n 25 --> f0b6f578-050f-4936-9ee7-9956b0760c6f;\n style f0b6f578-050f-4936-9ee7-9956b0760c6f stroke:#2c3143,stroke-width:4px;\n 26[\"Scanpy ComputeGraph\"];\n 24 -->|output_h5ad| 26;\n 27[\"Scanpy RunTSNE\"];\n 26 -->|output_h5ad| 27;\n 28[\"Scanpy RunUMAP\"];\n 27 -->|output_h5ad| 28;\n 29[\"Scanpy FindCluster\"];\n 28 -->|output_h5ad| 29;\n 30[\"Scanpy FindMarkers\"];\n 29 -->|output_h5ad| 30;\n 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3[\"Output\\nMarkers - cluster\"];\n 30 --> 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3;\n style 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3 stroke:#2c3143,stroke-width:4px;\n 98e98405-951e-4c6c-be01-3c925ae35449[\"Output\\nFinal object\"];\n 30 --> 98e98405-951e-4c6c-be01-3c925ae35449;\n style 98e98405-951e-4c6c-be01-3c925ae35449 stroke:#2c3143,stroke-width:4px;\n 31[\"Scanpy FindMarkers\"];\n 29 -->|output_h5ad| 31;\n 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4[\"Output\\nMarkers - genotype\"];\n 31 --> 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4;\n style 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4 stroke:#2c3143,stroke-width:4px;\n 32[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 32;\n 33[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 33;\n 34[\"Manipulate AnnData\"];\n 30 -->|output_h5ad| 34;\n 35[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 35;\n 36[\"Inspect AnnData\"];\n 30 -->|output_h5ad| 36;\n 37[\"AnnData Operations\"];\n 34 -->|anndata| 37;\n 30 -->|output_h5ad| 37;\n 38[\"Join two Datasets\"];\n 30 -->|output_tsv| 38;\n 36 -->|var| 38;\n 39[\"Join two Datasets\"];\n 31 -->|output_tsv| 39;\n 36 -->|var| 39;\n 40[\"AnnData Operations\"];\n 37 -->|output_h5ad| 40;\n 10bd70f8-ffcb-442b-9647-e5b947b6d35e[\"Output\\nFinal cell annotated object\"];\n 40 --> 10bd70f8-ffcb-442b-9647-e5b947b6d35e;\n style 10bd70f8-ffcb-442b-9647-e5b947b6d35e stroke:#2c3143,stroke-width:4px;\n 41[\"Cut\"];\n 38 -->|out_file1| 41;\n 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e[\"Output\\nMarkers - cluster - named\"];\n 41 --> 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e;\n style 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e stroke:#2c3143,stroke-width:4px;\n 42[\"Cut\"];\n 39 -->|out_file1| 42;\n 3b471f3d-263d-4299-9b7d-8a8ae1aa556e[\"Output\\nMarkers - genotype - named\"];\n 42 --> 3b471f3d-263d-4299-9b7d-8a8ae1aa556e;\n style 3b471f3d-263d-4299-9b7d-8a8ae1aa556e stroke:#2c3143,stroke-width:4px;\n 43[\"Scanpy PlotEmbed\"];\n 40 -->|output_h5ad| 43;",
- "modified": "2024-06-24 00:06:33 +0000",
- "name": "Filter, Plot and Explore Single-cell RNA-seq Data updated",
- "path": "topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/Filter,-Plot-and-Explore-Single-cell-RNA-seq-Data-updated.ga",
- "test_results": null,
- "tests": true,
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- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nExpression matrix input\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nCell annotations input\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nGene annotations input\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Monocle3 create\"];\n 1 -->|output| 3;\n 0 -->|output| 3;\n 2 -->|output| 3;\n 30db218d-f9e5-426d-ac9b-7823743ab5fb[\"Output\\nMonocle3 create on input dataset(s): cds3\"];\n 3 --> 30db218d-f9e5-426d-ac9b-7823743ab5fb;\n style 30db218d-f9e5-426d-ac9b-7823743ab5fb stroke:#2c3143,stroke-width:4px;\n 4[\"Monocle3 preprocess\"];\n 3 -->|output_rds| 4;\n 38996ee0-0c00-4a01-ad18-f2e505eaf780[\"Output\\nMonocle3 preprocess on input dataset(s): cds3\"];\n 4 --> 38996ee0-0c00-4a01-ad18-f2e505eaf780;\n style 38996ee0-0c00-4a01-ad18-f2e505eaf780 stroke:#2c3143,stroke-width:4px;\n 5[\"Monocle3 reduceDim\"];\n 4 -->|output_rds| 5;\n 21edf68f-72df-457d-aad7-c5fc5afa2b6b[\"Output\\nMonocle3 reduceDim on input dataset(s): cds3\"];\n 5 --> 21edf68f-72df-457d-aad7-c5fc5afa2b6b;\n style 21edf68f-72df-457d-aad7-c5fc5afa2b6b stroke:#2c3143,stroke-width:4px;\n 6[\"Monocle3 partition\"];\n 5 -->|output_rds| 6;\n fdb0e520-27c4-43a0-8f27-a25832a0816d[\"Output\\nMonocle3 partition on input dataset(s): cds3\"];\n 6 --> fdb0e520-27c4-43a0-8f27-a25832a0816d;\n style fdb0e520-27c4-43a0-8f27-a25832a0816d stroke:#2c3143,stroke-width:4px;\n 7[\"Plot cell type\"];\n 5 -->|output_rds| 7;\n 5e309658-e20f-4da1-8841-818f16fa8f01[\"Output\\nCell type plot\"];\n 7 --> 5e309658-e20f-4da1-8841-818f16fa8f01;\n style 5e309658-e20f-4da1-8841-818f16fa8f01 stroke:#2c3143,stroke-width:4px;\n 8[\"Plot genotype\"];\n 5 -->|output_rds| 8;\n aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4[\"Output\\nGenotype plot\"];\n 8 --> aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4;\n style aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4 stroke:#2c3143,stroke-width:4px;\n 9[\"Plot batch\"];\n 5 -->|output_rds| 9;\n c8eec2e4-1a64-47bb-812b-4002968c57c8[\"Output\\nBatch plot\"];\n 9 --> c8eec2e4-1a64-47bb-812b-4002968c57c8;\n style c8eec2e4-1a64-47bb-812b-4002968c57c8 stroke:#2c3143,stroke-width:4px;\n 10[\"Plot sex\"];\n 5 -->|output_rds| 10;\n c75954dd-34d5-4a20-bcf3-e5cd92d74885[\"Output\\nSex plot\"];\n 10 --> c75954dd-34d5-4a20-bcf3-e5cd92d74885;\n style c75954dd-34d5-4a20-bcf3-e5cd92d74885 stroke:#2c3143,stroke-width:4px;\n 11[\"Monocle3 top markers\"];\n 6 -->|output_rds| 11;\n 12[\"Plot genes\"];\n 6 -->|output_rds| 12;\n f91c22a3-8c6d-432a-92c5-cb010115fa86[\"Output\\nGene expression plot\"];\n 12 --> f91c22a3-8c6d-432a-92c5-cb010115fa86;\n style f91c22a3-8c6d-432a-92c5-cb010115fa86 stroke:#2c3143,stroke-width:4px;\n 13[\"Plot partition\"];\n 6 -->|output_rds| 13;\n f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d[\"Output\\nPartition plot\"];\n 13 --> f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d;\n style f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d stroke:#2c3143,stroke-width:4px;\n 14[\"Plot cluster\"];\n 6 -->|output_rds| 14;\n a2c1a628-d79d-4e37-ad33-de92033021a8[\"Output\\nCluster plot\"];\n 14 --> a2c1a628-d79d-4e37-ad33-de92033021a8;\n style a2c1a628-d79d-4e37-ad33-de92033021a8 stroke:#2c3143,stroke-width:4px;\n 15[\"Monocle3 learnGraph\"];\n 6 -->|output_rds| 15;\n ed2003aa-4680-409f-8d79-e79b878a786c[\"Output\\nMonocle3 learnGraph on input dataset(s): cds3\"];\n 15 --> ed2003aa-4680-409f-8d79-e79b878a786c;\n style ed2003aa-4680-409f-8d79-e79b878a786c stroke:#2c3143,stroke-width:4px;\n 16[\"Plot learned trajectory\"];\n 15 -->|output_rds| 16;\n 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d[\"Output\\nCell types & learned trajectory path plot\"];\n 16 --> 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d;\n style 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d stroke:#2c3143,stroke-width:4px;\n 17[\"Monocle3 orderCells\"];\n 15 -->|output_rds| 17;\n 96d10412-3d7f-4970-b541-6f4367fa3f37[\"Output\\nMonocle3 orderCells on input dataset(s): cds3\"];\n 17 --> 96d10412-3d7f-4970-b541-6f4367fa3f37;\n style 96d10412-3d7f-4970-b541-6f4367fa3f37 stroke:#2c3143,stroke-width:4px;\n 18[\"Monocle3 diffExp\"];\n 17 -->|output_rds| 18;\n db1dc457-2d6e-47cc-b7ce-d0a4d23e9498[\"Output\\nDifferential expression of genes - table\"];\n 18 --> db1dc457-2d6e-47cc-b7ce-d0a4d23e9498;\n style db1dc457-2d6e-47cc-b7ce-d0a4d23e9498 stroke:#2c3143,stroke-width:4px;\n 19[\"Plot pseudotime\"];\n 17 -->|output_rds| 19;\n d1b3efd2-0a81-4dad-8652-589c2678fbaa[\"Output\\nPseudotime plot\"];\n 19 --> d1b3efd2-0a81-4dad-8652-589c2678fbaa;\n style d1b3efd2-0a81-4dad-8652-589c2678fbaa stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-06-24 00:06:33 +0000",
- "name": "Monocle3 workflow",
- "path": "topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Galaxy-Workflow-Monocle3_workflow.ga",
- "test_results": null,
- "tests": false,
- "title": "Monocle3 workflow",
- "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_monocle3-trajectories/versions/galaxy-workflow-monocle3_workflow",
- "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Galaxy-Workflow-Monocle3_workflow.ga",
- "wfid": "single-cell-scrna-case_monocle3-trajectories",
- "wfname": "galaxy-workflow-monocle3_workflow",
- "workflow": "Galaxy-Workflow-Monocle3_workflow.ga"
- },
- {
- "creators": [
- {
- "class": "Organization",
- "identifier": "0009-0001-2017-8805",
- "name": "Julia Jakiela"
- }
- ],
- "license": "CC-BY-4.0",
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAnnData to extract genes & cells annotations\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nAnnData before processing to extract clean expression matrix\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Extract cell annotations\"];\n 0 -->|output| 2;\n 0646798d-3a5d-420a-a7cf-cde6cec722d5[\"Output\\nExtracted cell annotations (obs)\"];\n 2 --> 0646798d-3a5d-420a-a7cf-cde6cec722d5;\n style 0646798d-3a5d-420a-a7cf-cde6cec722d5 stroke:#2c3143,stroke-width:4px;\n 3[\"Extract gene annotations\"];\n 0 -->|output| 3;\n 84162745-68b0-41a5-b06e-a285440ba095[\"Output\\nExtracted gene annotations (var)\"];\n 3 --> 84162745-68b0-41a5-b06e-a285440ba095;\n style 84162745-68b0-41a5-b06e-a285440ba095 stroke:#2c3143,stroke-width:4px;\n 4[\"Extract clean expression matrix\"];\n 1 -->|output| 4;\n 3f03af0c-ac41-4450-b5ba-639a79ea543b[\"Output\\nUnprocessed expression matrix\"];\n 4 --> 3f03af0c-ac41-4450-b5ba-639a79ea543b;\n style 3f03af0c-ac41-4450-b5ba-639a79ea543b stroke:#2c3143,stroke-width:4px;\n 5[\"Filter out macrophages\"];\n 2 -->|obs| 5;\n fb81e9a1-0603-419a-83f5-0c9f94939b16[\"Output\\nCells without macrophages\"];\n 5 --> fb81e9a1-0603-419a-83f5-0c9f94939b16;\n style fb81e9a1-0603-419a-83f5-0c9f94939b16 stroke:#2c3143,stroke-width:4px;\n 6[\"gene_short_name annotation\"];\n 3 -->|var| 6;\n 94a60e6c-cdf7-48e5-8b55-d221cef22688[\"Output\\nGenes table with gene_short_name colname\"];\n 6 --> 94a60e6c-cdf7-48e5-8b55-d221cef22688;\n style 94a60e6c-cdf7-48e5-8b55-d221cef22688 stroke:#2c3143,stroke-width:4px;\n 7[\"Cut cells IDs\"];\n 5 -->|out_file1| 7;\n 34146c30-2666-481f-8d49-a849d5d3aa91[\"Output\\nFiltered cells IDs \"];\n 7 --> 34146c30-2666-481f-8d49-a849d5d3aa91;\n style 34146c30-2666-481f-8d49-a849d5d3aa91 stroke:#2c3143,stroke-width:4px;\n 8[\"Cut genes IDs\"];\n 6 -->|out_file1| 8;\n 8f38fb93-cb30-4fbc-90c5-7f6bd023feea[\"Output\\nGenes IDs\"];\n 8 --> 8f38fb93-cb30-4fbc-90c5-7f6bd023feea;\n style 8f38fb93-cb30-4fbc-90c5-7f6bd023feea stroke:#2c3143,stroke-width:4px;\n 9[\"Filter matrix by cells\"];\n 7 -->|out_file1| 9;\n 4 -->|X| 9;\n f654c045-5fea-43f9-96d6-492c810593d2[\"Output\\nPre-filtered matrix (by cells)\"];\n 9 --> f654c045-5fea-43f9-96d6-492c810593d2;\n style f654c045-5fea-43f9-96d6-492c810593d2 stroke:#2c3143,stroke-width:4px;\n 10[\"Remove duplicate column cells IDs\"];\n 9 -->|out_file1| 10;\n f633c125-a4d0-4fa7-ab87-022349f4ac70[\"Output\\nFiltered matrix (by cells) \"];\n 10 --> f633c125-a4d0-4fa7-ab87-022349f4ac70;\n style f633c125-a4d0-4fa7-ab87-022349f4ac70 stroke:#2c3143,stroke-width:4px;\n 11[\"Transpose matrix\"];\n 10 -->|output| 11;\n 3202091e-1afc-4f50-8922-1f9e50c490fc[\"Output\\nfiltered matrix (by cells) transposed\"];\n 11 --> 3202091e-1afc-4f50-8922-1f9e50c490fc;\n style 3202091e-1afc-4f50-8922-1f9e50c490fc stroke:#2c3143,stroke-width:4px;\n 12[\"Filter matrix by genes\"];\n 8 -->|out_file1| 12;\n 11 -->|out_file| 12;\n 6c23cbd5-a1b5-428e-8ff9-ebac4893ad88[\"Output\\nPre-filtered matrix (by cells & genes)\"];\n 12 --> 6c23cbd5-a1b5-428e-8ff9-ebac4893ad88;\n style 6c23cbd5-a1b5-428e-8ff9-ebac4893ad88 stroke:#2c3143,stroke-width:4px;\n 13[\"Remove duplicate column genes IDs\"];\n 12 -->|out_file1| 13;\n 25839326-0b5d-4e74-91ec-24e22c08f7c5[\"Output\\nFiltered matrix (by cells & genes)\"];\n 13 --> 25839326-0b5d-4e74-91ec-24e22c08f7c5;\n style 25839326-0b5d-4e74-91ec-24e22c08f7c5 stroke:#2c3143,stroke-width:4px;\n 14[\"Monocle3 create\"];\n 5 -->|out_file1| 14;\n 13 -->|output| 14;\n 6 -->|out_file1| 14;\n f8c5589c-a70d-416e-a9de-ebc987f61fc3[\"Output\\nMonocle3 create on input dataset(s): cds3\"];\n 14 --> f8c5589c-a70d-416e-a9de-ebc987f61fc3;\n style f8c5589c-a70d-416e-a9de-ebc987f61fc3 stroke:#2c3143,stroke-width:4px;\n 15[\"Monocle3 preprocess\"];\n 14 -->|output_rds| 15;\n c134942f-60e7-4cd0-8c32-da4a303b879d[\"Output\\nMonocle3 preprocess on input dataset(s): cds3\"];\n 15 --> c134942f-60e7-4cd0-8c32-da4a303b879d;\n style c134942f-60e7-4cd0-8c32-da4a303b879d stroke:#2c3143,stroke-width:4px;\n 16[\"Monocle3 reduceDim\"];\n 15 -->|output_rds| 16;\n 2c9fb108-2a1c-41df-a8d8-81a18b66d2a1[\"Output\\nMonocle3 reduceDim on input dataset(s): cds3\"];\n 16 --> 2c9fb108-2a1c-41df-a8d8-81a18b66d2a1;\n style 2c9fb108-2a1c-41df-a8d8-81a18b66d2a1 stroke:#2c3143,stroke-width:4px;\n 17[\"Monocle3 partition\"];\n 16 -->|output_rds| 17;\n 93371c10-6583-47fc-830f-9a90dc980766[\"Output\\nMonocle3 partition on input dataset(s): cds3\"];\n 17 --> 93371c10-6583-47fc-830f-9a90dc980766;\n style 93371c10-6583-47fc-830f-9a90dc980766 stroke:#2c3143,stroke-width:4px;\n 18[\"Plot cell type\"];\n 16 -->|output_rds| 18;\n f096d060-82e8-4847-9e8f-b22c9288f565[\"Output\\nCell type plot\"];\n 18 --> f096d060-82e8-4847-9e8f-b22c9288f565;\n style f096d060-82e8-4847-9e8f-b22c9288f565 stroke:#2c3143,stroke-width:4px;\n 19[\"Plot genotype\"];\n 16 -->|output_rds| 19;\n aab28bb1-e2e7-4b7d-9b2b-1cab64bea287[\"Output\\nGenotype plot\"];\n 19 --> aab28bb1-e2e7-4b7d-9b2b-1cab64bea287;\n style aab28bb1-e2e7-4b7d-9b2b-1cab64bea287 stroke:#2c3143,stroke-width:4px;\n 20[\"Plot batch\"];\n 16 -->|output_rds| 20;\n 9b362eee-9238-47c5-a4c2-85f3995430f4[\"Output\\nBatch plot\"];\n 20 --> 9b362eee-9238-47c5-a4c2-85f3995430f4;\n style 9b362eee-9238-47c5-a4c2-85f3995430f4 stroke:#2c3143,stroke-width:4px;\n 21[\"Plot sex\"];\n 16 -->|output_rds| 21;\n c2a1e104-ef2d-4b66-ac2b-bf0251714434[\"Output\\nSex plot\"];\n 21 --> c2a1e104-ef2d-4b66-ac2b-bf0251714434;\n style c2a1e104-ef2d-4b66-ac2b-bf0251714434 stroke:#2c3143,stroke-width:4px;\n 22[\"Monocle3 top markers\"];\n 17 -->|output_rds| 22;\n 23[\"Plot genes\"];\n 17 -->|output_rds| 23;\n e8867379-82c6-4c32-a2d3-0b24670269ae[\"Output\\nGene expression plot\"];\n 23 --> e8867379-82c6-4c32-a2d3-0b24670269ae;\n style e8867379-82c6-4c32-a2d3-0b24670269ae stroke:#2c3143,stroke-width:4px;\n 24[\"Plot partition\"];\n 17 -->|output_rds| 24;\n 3f7b0a7c-85d6-430b-8385-fa9a76385c0e[\"Output\\nPartition plot\"];\n 24 --> 3f7b0a7c-85d6-430b-8385-fa9a76385c0e;\n style 3f7b0a7c-85d6-430b-8385-fa9a76385c0e stroke:#2c3143,stroke-width:4px;\n 25[\"Plot cluster\"];\n 17 -->|output_rds| 25;\n 40b65826-f73e-4054-a56d-b241985d6996[\"Output\\nCluster plot\"];\n 25 --> 40b65826-f73e-4054-a56d-b241985d6996;\n style 40b65826-f73e-4054-a56d-b241985d6996 stroke:#2c3143,stroke-width:4px;\n 26[\"Monocle3 learnGraph\"];\n 17 -->|output_rds| 26;\n 294b1a49-cec6-49d0-bcd4-3a954da67bec[\"Output\\nMonocle3 learnGraph on input dataset(s): cds3\"];\n 26 --> 294b1a49-cec6-49d0-bcd4-3a954da67bec;\n style 294b1a49-cec6-49d0-bcd4-3a954da67bec stroke:#2c3143,stroke-width:4px;\n 27[\"Plot learned trajectory\"];\n 26 -->|output_rds| 27;\n c85ddefe-8eaf-4d21-93ed-ca0859286bf0[\"Output\\nCell types & learned trajectory path plot\"];\n 27 --> c85ddefe-8eaf-4d21-93ed-ca0859286bf0;\n style c85ddefe-8eaf-4d21-93ed-ca0859286bf0 stroke:#2c3143,stroke-width:4px;\n 28[\"Monocle3 orderCells\"];\n 26 -->|output_rds| 28;\n 5aea5752-b767-4fc8-8741-1f4d1c659a41[\"Output\\nMonocle3 orderCells on input dataset(s): cds3\"];\n 28 --> 5aea5752-b767-4fc8-8741-1f4d1c659a41;\n style 5aea5752-b767-4fc8-8741-1f4d1c659a41 stroke:#2c3143,stroke-width:4px;\n 29[\"Monocle3 diffExp\"];\n 28 -->|output_rds| 29;\n 3c298624-9f06-4e52-b2a8-fb834b87c296[\"Output\\nDifferential expression of genes - table\"];\n 29 --> 3c298624-9f06-4e52-b2a8-fb834b87c296;\n style 3c298624-9f06-4e52-b2a8-fb834b87c296 stroke:#2c3143,stroke-width:4px;\n 30[\"Plot pseudotime\"];\n 28 -->|output_rds| 30;\n 813d15bb-0771-4aed-9226-4874c1ddba59[\"Output\\nPseudotime plot\"];\n 30 --> 813d15bb-0771-4aed-9226-4874c1ddba59;\n style 813d15bb-0771-4aed-9226-4874c1ddba59 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-06-24 00:06:33 +0000",
- "name": "Trajectory analysis using Monocle3 - full tutorial workflow",
- "path": "topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Trajectory-analysis-using-Monocle3---full-tutorial-workflow.ga",
- "test_results": null,
- "tests": true,
- "title": "Trajectory analysis using Monocle3 - full tutorial workflow",
- "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_monocle3-trajectories/versions/trajectory-analysis-using-monocle3---full-tutorial-workflow",
- "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Trajectory-analysis-using-Monocle3---full-tutorial-workflow.ga",
- "wfid": "single-cell-scrna-case_monocle3-trajectories",
- "wfname": "trajectory-analysis-using-monocle3---full-tutorial-workflow",
- "workflow": "Trajectory-analysis-using-Monocle3---full-tutorial-workflow.ga"
- }
- ],
- "zenodo_link": "https://zenodo.org/records/10397366"
- },
- {
- "admin_install": {
- "install_repository_dependencies": true,
- "install_resolver_dependencies": true,
- "install_tool_dependencies": true,
- "tools": [
- {
- "name": "music_construct_eset",
- "owner": "bgruening",
- "revisions": "282819d09a4f",
- "tool_panel_section_label": "Single-cell",
- "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
- },
- {
- "name": "music_manipulate_eset",
- "owner": "bgruening",
- "revisions": "22232092be53",
- "tool_panel_section_label": "Single-cell",
- "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
- },
- {
- "name": "text_processing",
- "owner": "bgruening",
- "revisions": "d698c222f354",
- "tool_panel_section_label": "Text Manipulation",
- "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
- },
- {
- "name": "text_processing",
- "owner": "bgruening",
- "revisions": "d698c222f354",
- "tool_panel_section_label": "Text Manipulation",
- "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
- },
- {
- "name": "text_processing",
- "owner": "bgruening",
- "revisions": "d698c222f354",
- "tool_panel_section_label": "Text Manipulation",
- "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
- },
- {
- "name": "text_processing",
- "owner": "bgruening",
- "revisions": "d698c222f354",
- "tool_panel_section_label": "Text Manipulation",
- "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
- },
- {
- "name": "regex_find_replace",
- "owner": "galaxyp",
- "revisions": "399da6b5ec21",
- "tool_panel_section_label": "Text Manipulation",
- "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
- },
- {
- "name": "annotatemyids",
- "owner": "iuc",
- "revisions": "fe3ca740a485",
- "tool_panel_section_label": "Annotation",
- "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
- },
- {
- "name": "column_remove_by_header",
- "owner": "iuc",
- "revisions": "2040e4c2750a",
- "tool_panel_section_label": "Text Manipulation",
- "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
- },
- {
- "name": "table_compute",
- "owner": "iuc",
- "revisions": "3bf5661c0280",
- "tool_panel_section_label": "Text Manipulation",
- "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
- }
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#171: KMP_AFFINITY: OS proc 57 maps to package 57 \nOMP: Info #171: KMP_AFFINITY: OS proc 58 maps to package 58 \nOMP: Info #171: KMP_AFFINITY: OS proc 59 maps to package 59 \nOMP: Info #171: KMP_AFFINITY: OS proc 60 maps to package 60 \nOMP: Info #171: KMP_AFFINITY: OS proc 61 maps to package 61 \nOMP: Info #171: KMP_AFFINITY: OS proc 62 maps to package 62 \nOMP: Info #171: KMP_AFFINITY: OS proc 63 maps to package 63 \nOMP: Info #171: KMP_AFFINITY: OS proc 64 maps to package 64 \nOMP: Info #171: KMP_AFFINITY: OS proc 65 maps to package 65 \nOMP: Info #171: KMP_AFFINITY: OS proc 66 maps to package 66 \nOMP: Info #171: KMP_AFFINITY: OS proc 67 maps to package 67 \nOMP: Info #171: KMP_AFFINITY: OS proc 68 maps to package 68 \nOMP: Info #171: KMP_AFFINITY: OS proc 69 maps to package 69 \nOMP: Info #171: KMP_AFFINITY: OS proc 70 maps to package 70 \nOMP: Info #171: KMP_AFFINITY: OS proc 71 maps to package 71 \nOMP: Info #171: KMP_AFFINITY: OS proc 72 maps to package 72 \nOMP: Info #171: KMP_AFFINITY: OS proc 73 maps to package 73 \nOMP: Info #171: KMP_AFFINITY: OS proc 74 maps to package 74 \nOMP: Info #171: KMP_AFFINITY: OS proc 75 maps to package 75 \nOMP: Info #171: KMP_AFFINITY: OS proc 76 maps to package 76 \nOMP: Info #171: KMP_AFFINITY: OS proc 77 maps to package 77 \nOMP: Info #171: KMP_AFFINITY: OS proc 78 maps to package 78 \nOMP: Info #171: KMP_AFFINITY: OS proc 79 maps to package 79 \nOMP: Info #171: KMP_AFFINITY: OS proc 80 maps to package 80 \nOMP: Info #171: KMP_AFFINITY: OS proc 81 maps to package 81 \nOMP: Info #171: KMP_AFFINITY: OS proc 82 maps to package 82 \nOMP: Info #171: KMP_AFFINITY: OS proc 83 maps to package 83 \nOMP: Info #171: KMP_AFFINITY: OS proc 84 maps to package 84 \nOMP: Info #171: KMP_AFFINITY: OS proc 85 maps to package 85 \nOMP: Info #171: KMP_AFFINITY: OS proc 86 maps to package 86 \nOMP: Info #171: KMP_AFFINITY: OS proc 87 maps to package 87 \nOMP: Info #171: KMP_AFFINITY: OS proc 88 maps to package 88 \nOMP: Info #171: KMP_AFFINITY: OS proc 89 maps to package 89 \nOMP: Info #171: KMP_AFFINITY: OS proc 90 maps to package 90 \nOMP: Info #171: KMP_AFFINITY: OS proc 91 maps to package 91 \nOMP: Info #171: KMP_AFFINITY: OS proc 92 maps to package 92 \nOMP: Info #171: KMP_AFFINITY: OS proc 93 maps to package 93 \nOMP: Info #171: KMP_AFFINITY: OS proc 94 maps to package 94 \nOMP: Info #171: KMP_AFFINITY: OS proc 95 maps to package 95 \nOMP: Info #171: KMP_AFFINITY: OS proc 96 maps to package 96 \nOMP: Info #171: KMP_AFFINITY: OS proc 97 maps to package 97 \nOMP: Info #171: KMP_AFFINITY: OS proc 98 maps to package 98 \nOMP: Info #171: KMP_AFFINITY: OS proc 99 maps to package 99 \nOMP: Info #171: KMP_AFFINITY: OS proc 100 maps to package 100 \nOMP: Info #171: KMP_AFFINITY: OS proc 101 maps to package 101 \nOMP: Info #171: KMP_AFFINITY: OS proc 102 maps to package 102 \nOMP: Info #171: KMP_AFFINITY: OS proc 103 maps to package 103 \nOMP: Info #171: KMP_AFFINITY: OS proc 104 maps to package 104 \nOMP: Info #171: KMP_AFFINITY: OS proc 105 maps to package 105 \nOMP: Info #171: KMP_AFFINITY: OS proc 106 maps to package 106 \nOMP: Info #171: KMP_AFFINITY: OS proc 107 maps to package 107 \nOMP: Info #171: KMP_AFFINITY: OS proc 108 maps to package 108 \nOMP: Info #171: KMP_AFFINITY: OS proc 109 maps to package 109 \nOMP: Info #171: KMP_AFFINITY: OS proc 110 maps to package 110 \nOMP: Info #171: KMP_AFFINITY: OS proc 111 maps to package 111 \nOMP: Info #171: KMP_AFFINITY: OS proc 112 maps to package 112 \nOMP: Info #171: KMP_AFFINITY: OS proc 113 maps to package 113 \nOMP: Info #171: KMP_AFFINITY: OS proc 114 maps to package 114 \nOMP: Info #171: KMP_AFFINITY: OS proc 115 maps to package 115 \nOMP: Info #171: KMP_AFFINITY: OS proc 116 maps to package 116 \nOMP: Info #171: KMP_AFFINITY: OS proc 117 maps to package 117 \nOMP: Info #171: KMP_AFFINITY: OS proc 118 maps to package 118 \nOMP: Info #171: KMP_AFFINITY: OS proc 119 maps to package 119 \nOMP: Info #171: KMP_AFFINITY: OS proc 120 maps to package 120 \nOMP: Info #171: KMP_AFFINITY: OS proc 121 maps to package 121 \nOMP: Info #171: KMP_AFFINITY: OS proc 122 maps to package 122 \nOMP: Info #171: KMP_AFFINITY: OS proc 123 maps to package 123 \nOMP: Info #171: KMP_AFFINITY: OS proc 124 maps to package 124 \nOMP: Info #250: KMP_AFFINITY: pid 2936157 tid 2936157 thread 0 bound to OS proc set 0\nUsing TensorFlow backend.\n/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.\n warnings.warn(msg, category=DeprecationWarning)\n",
- "stdout": "",
- "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1",
- "tool_stderr": "OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids.\nOMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info\nOMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 0-124\nOMP: Info #156: KMP_AFFINITY: 125 available OS procs\nOMP: Info #157: KMP_AFFINITY: Uniform topology\nOMP: Info #179: KMP_AFFINITY: 125 packages x 1 cores/pkg x 1 threads/core (125 total cores)\nOMP: Info #214: KMP_AFFINITY: OS proc to physical thread map:\nOMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 \nOMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 1 \nOMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 2 \nOMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 3 \nOMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 4 \nOMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 5 \nOMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 6 \nOMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 7 \nOMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 8 \nOMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 9 \nOMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 10 \nOMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 11 \nOMP: Info #171: KMP_AFFINITY: OS proc 12 maps to package 12 \nOMP: Info #171: KMP_AFFINITY: OS proc 13 maps to package 13 \nOMP: Info #171: KMP_AFFINITY: OS proc 14 maps to package 14 \nOMP: Info #171: KMP_AFFINITY: OS proc 15 maps to package 15 \nOMP: Info #171: KMP_AFFINITY: OS proc 16 maps to package 16 \nOMP: Info #171: KMP_AFFINITY: OS proc 17 maps to package 17 \nOMP: Info #171: KMP_AFFINITY: OS proc 18 maps to package 18 \nOMP: Info #171: KMP_AFFINITY: OS proc 19 maps to package 19 \nOMP: Info #171: KMP_AFFINITY: OS proc 20 maps to package 20 \nOMP: Info #171: KMP_AFFINITY: OS proc 21 maps to package 21 \nOMP: Info #171: KMP_AFFINITY: OS proc 22 maps to package 22 \nOMP: Info #171: KMP_AFFINITY: OS proc 23 maps to package 23 \nOMP: Info #171: KMP_AFFINITY: OS proc 24 maps to package 24 \nOMP: Info #171: KMP_AFFINITY: OS proc 25 maps to package 25 \nOMP: Info #171: KMP_AFFINITY: OS proc 26 maps to package 26 \nOMP: Info #171: KMP_AFFINITY: OS proc 27 maps to package 27 \nOMP: Info #171: KMP_AFFINITY: OS proc 28 maps to package 28 \nOMP: Info #171: KMP_AFFINITY: OS proc 29 maps to package 29 \nOMP: Info #171: KMP_AFFINITY: OS proc 30 maps to package 30 \nOMP: Info #171: KMP_AFFINITY: OS proc 31 maps to package 31 \nOMP: Info #171: KMP_AFFINITY: OS proc 32 maps to package 32 \nOMP: Info #171: KMP_AFFINITY: OS proc 33 maps to package 33 \nOMP: Info #171: KMP_AFFINITY: OS proc 34 maps to package 34 \nOMP: Info #171: KMP_AFFINITY: OS proc 35 maps to package 35 \nOMP: Info #171: KMP_AFFINITY: OS proc 36 maps to package 36 \nOMP: Info #171: KMP_AFFINITY: OS proc 37 maps to package 37 \nOMP: Info #171: KMP_AFFINITY: OS proc 38 maps to package 38 \nOMP: Info #171: KMP_AFFINITY: OS proc 39 maps to package 39 \nOMP: Info #171: KMP_AFFINITY: OS proc 40 maps to package 40 \nOMP: Info #171: KMP_AFFINITY: OS proc 41 maps to package 41 \nOMP: Info #171: KMP_AFFINITY: OS proc 42 maps to package 42 \nOMP: Info #171: KMP_AFFINITY: OS proc 43 maps to package 43 \nOMP: Info #171: KMP_AFFINITY: OS proc 44 maps to package 44 \nOMP: Info #171: KMP_AFFINITY: OS proc 45 maps to package 45 \nOMP: Info #171: KMP_AFFINITY: OS proc 46 maps to package 46 \nOMP: Info #171: KMP_AFFINITY: OS proc 47 maps to package 47 \nOMP: Info #171: KMP_AFFINITY: OS proc 48 maps to package 48 \nOMP: Info #171: KMP_AFFINITY: OS proc 49 maps to package 49 \nOMP: Info #171: KMP_AFFINITY: OS proc 50 maps to package 50 \nOMP: Info #171: KMP_AFFINITY: OS proc 51 maps to package 51 \nOMP: Info #171: KMP_AFFINITY: OS proc 52 maps to package 52 \nOMP: Info #171: KMP_AFFINITY: OS proc 53 maps to package 53 \nOMP: Info #171: KMP_AFFINITY: OS proc 54 maps to package 54 \nOMP: Info #171: KMP_AFFINITY: OS proc 55 maps to package 55 \nOMP: Info #171: KMP_AFFINITY: OS proc 56 maps to package 56 \nOMP: Info #171: KMP_AFFINITY: OS proc 57 maps to package 57 \nOMP: Info #171: KMP_AFFINITY: OS proc 58 maps to package 58 \nOMP: Info #171: KMP_AFFINITY: OS proc 59 maps to package 59 \nOMP: Info #171: KMP_AFFINITY: OS proc 60 maps to package 60 \nOMP: Info #171: KMP_AFFINITY: OS proc 61 maps to package 61 \nOMP: Info #171: KMP_AFFINITY: OS proc 62 maps to package 62 \nOMP: Info #171: KMP_AFFINITY: OS proc 63 maps to package 63 \nOMP: Info #171: KMP_AFFINITY: OS proc 64 maps to package 64 \nOMP: Info #171: KMP_AFFINITY: OS proc 65 maps to package 65 \nOMP: Info #171: KMP_AFFINITY: OS proc 66 maps to package 66 \nOMP: Info #171: KMP_AFFINITY: OS proc 67 maps to package 67 \nOMP: Info #171: KMP_AFFINITY: OS proc 68 maps to package 68 \nOMP: Info #171: KMP_AFFINITY: OS proc 69 maps to package 69 \nOMP: Info #171: KMP_AFFINITY: OS proc 70 maps to package 70 \nOMP: Info #171: KMP_AFFINITY: OS proc 71 maps to package 71 \nOMP: Info #171: KMP_AFFINITY: OS proc 72 maps to package 72 \nOMP: Info #171: KMP_AFFINITY: OS proc 73 maps to package 73 \nOMP: Info #171: KMP_AFFINITY: OS proc 74 maps to package 74 \nOMP: Info #171: KMP_AFFINITY: OS proc 75 maps to package 75 \nOMP: Info #171: KMP_AFFINITY: OS proc 76 maps to package 76 \nOMP: Info #171: KMP_AFFINITY: OS proc 77 maps to package 77 \nOMP: Info #171: KMP_AFFINITY: OS proc 78 maps to package 78 \nOMP: Info #171: KMP_AFFINITY: OS proc 79 maps to package 79 \nOMP: Info #171: KMP_AFFINITY: OS proc 80 maps to package 80 \nOMP: Info #171: KMP_AFFINITY: OS proc 81 maps to package 81 \nOMP: Info #171: KMP_AFFINITY: OS proc 82 maps to package 82 \nOMP: Info #171: KMP_AFFINITY: OS proc 83 maps to package 83 \nOMP: Info #171: KMP_AFFINITY: OS proc 84 maps to package 84 \nOMP: Info #171: KMP_AFFINITY: OS proc 85 maps to package 85 \nOMP: Info #171: KMP_AFFINITY: OS proc 86 maps to package 86 \nOMP: Info #171: KMP_AFFINITY: OS proc 87 maps to package 87 \nOMP: Info #171: KMP_AFFINITY: OS proc 88 maps to package 88 \nOMP: Info #171: KMP_AFFINITY: OS proc 89 maps to package 89 \nOMP: Info #171: KMP_AFFINITY: OS proc 90 maps to package 90 \nOMP: Info #171: KMP_AFFINITY: OS proc 91 maps to package 91 \nOMP: Info #171: KMP_AFFINITY: OS proc 92 maps to package 92 \nOMP: Info #171: KMP_AFFINITY: OS proc 93 maps to package 93 \nOMP: Info #171: KMP_AFFINITY: OS proc 94 maps to package 94 \nOMP: Info #171: KMP_AFFINITY: OS proc 95 maps to package 95 \nOMP: Info #171: KMP_AFFINITY: OS proc 96 maps to package 96 \nOMP: Info #171: KMP_AFFINITY: OS proc 97 maps to package 97 \nOMP: Info #171: KMP_AFFINITY: OS proc 98 maps to package 98 \nOMP: Info #171: KMP_AFFINITY: OS proc 99 maps to package 99 \nOMP: Info #171: KMP_AFFINITY: OS proc 100 maps to package 100 \nOMP: Info #171: KMP_AFFINITY: OS proc 101 maps to package 101 \nOMP: Info #171: KMP_AFFINITY: OS proc 102 maps to package 102 \nOMP: Info #171: KMP_AFFINITY: OS proc 103 maps to package 103 \nOMP: Info #171: KMP_AFFINITY: OS proc 104 maps to package 104 \nOMP: Info #171: KMP_AFFINITY: OS proc 105 maps to package 105 \nOMP: Info #171: KMP_AFFINITY: OS proc 106 maps to package 106 \nOMP: Info #171: KMP_AFFINITY: OS proc 107 maps to package 107 \nOMP: Info #171: KMP_AFFINITY: OS proc 108 maps to package 108 \nOMP: Info #171: KMP_AFFINITY: OS proc 109 maps to package 109 \nOMP: Info #171: KMP_AFFINITY: OS proc 110 maps to package 110 \nOMP: Info #171: KMP_AFFINITY: OS proc 111 maps to package 111 \nOMP: Info #171: KMP_AFFINITY: OS proc 112 maps to package 112 \nOMP: Info #171: KMP_AFFINITY: OS proc 113 maps to package 113 \nOMP: Info #171: KMP_AFFINITY: OS proc 114 maps to package 114 \nOMP: Info #171: KMP_AFFINITY: OS proc 115 maps to package 115 \nOMP: Info #171: KMP_AFFINITY: OS proc 116 maps to package 116 \nOMP: Info #171: KMP_AFFINITY: OS proc 117 maps to package 117 \nOMP: Info #171: KMP_AFFINITY: OS proc 118 maps to package 118 \nOMP: Info #171: KMP_AFFINITY: OS proc 119 maps to package 119 \nOMP: Info #171: KMP_AFFINITY: OS proc 120 maps to package 120 \nOMP: Info #171: KMP_AFFINITY: OS proc 121 maps to package 121 \nOMP: Info #171: KMP_AFFINITY: OS proc 122 maps to package 122 \nOMP: Info #171: KMP_AFFINITY: OS proc 123 maps to package 123 \nOMP: Info #171: KMP_AFFINITY: OS proc 124 maps to package 124 \nOMP: Info #250: KMP_AFFINITY: pid 2936157 tid 2936157 thread 0 bound to OS proc set 0\nUsing TensorFlow backend.\n/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.\n warnings.warn(msg, category=DeprecationWarning)\n",
- "tool_stdout": "",
- "traceback": null,
- "update_time": "2023-05-23T11:03:10.618603",
- "user_email": "hxr@informatik.uni-freiburg.de"
- }
- ],
- "model_class": "WorkflowInvocationStep",
- "order_index": 2,
- "output_collections": {},
- "outputs": {
- "outfile_fit": {
- "id": "4838ba20a6d86765b565f48d5ac913b1",
- "src": "hda",
- "uuid": "1a17ebe9-c0e0-4ebd-bae0-5159331683bb"
- }
- },
- "state": "scheduled",
- "subworkflow": null,
- "subworkflow_invocation_id": null,
- "update_time": "2023-05-23T11:03:10.590397",
- "workflow_step_id": "3500dc3fab19a665",
- "workflow_step_label": null,
- "workflow_step_uuid": "159f5d0f-2ff6-46f3-8e42-7b7c1f9c346e"
- },
- "3. Unnamed step": {
- "action": null,
- "id": "06d0cb6c722a3ad0",
- "job_id": "11ac94870d0bb33a7b20a18462093261",
- "jobs": [
- {
- "command_line": "python '/data/jwd02f/main/060/156/60156805/configs/tmpsg_iolk6' '/data/jwd02f/main/060/156/60156805/configs/tmpbg5s306r'",
- "command_version": "1.0.8.1",
- "create_time": "2023-05-23T10:59:49.663928",
- "dependencies": [
- {
- "cacheable": false,
- "dependency_resolver": {
- "auto_init": true,
- "auto_install": false,
- "can_uninstall_dependencies": true,
- "ensure_channels": "conda-forge,bioconda",
- "model_class": "CondaDependencyResolver",
- "prefix": "/usr/local/tools/_conda",
- "read_only": false,
- "resolver_type": "conda",
- "resolves_simple_dependencies": true,
- "use_local": false,
- "versionless": false
- },
- "dependency_type": "conda",
- "environment_path": "/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59",
- "exact": true,
- "model_class": "MergedCondaDependency",
- "name": "python",
- "version": "3.6"
- },
- {
- "cacheable": false,
- "dependency_resolver": {
- "auto_init": true,
- "auto_install": false,
- "can_uninstall_dependencies": true,
- "ensure_channels": "conda-forge,bioconda",
- "model_class": "CondaDependencyResolver",
- "prefix": "/usr/local/tools/_conda",
- "read_only": false,
- "resolver_type": "conda",
- "resolves_simple_dependencies": true,
- "use_local": false,
- "versionless": false
- },
- "dependency_type": "conda",
- "environment_path": "/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59",
- "exact": true,
- "model_class": "MergedCondaDependency",
- "name": "Galaxy-ML",
- "version": "0.8.1"
- }
- ],
- "exit_code": 0,
- "external_id": "43631439",
- "galaxy_version": "23.0",
- "history_id": "2507553dd7587c83",
- "id": "11ac94870d0bb33a7b20a18462093261",
- "inputs": {
- "infile_data": {
- "id": "4838ba20a6d867654de1bc22fefb9f52",
- "src": "hda",
- "uuid": "c438049f-86b6-415a-a9a0-554efa397b28"
- },
- "infile_model": {
- "id": "4838ba20a6d86765b565f48d5ac913b1",
- "src": "hda",
- "uuid": "1a17ebe9-c0e0-4ebd-bae0-5159331683bb"
- }
- },
- "job_messages": [],
- "job_metrics": [
- {
- "name": "hostname",
- "plugin": "hostname",
- "raw_value": "vgcnbwc-worker-c28m475-9818.novalocal",
- "title": "hostname",
- "value": "vgcnbwc-worker-c28m475-9818.novalocal"
- },
- {
- "name": "galaxy_slots",
- "plugin": "core",
- "raw_value": "1.0000000",
- "title": "Cores Allocated",
- "value": "1"
- },
- {
- "name": "galaxy_memory_mb",
- "plugin": "core",
- "raw_value": "3891.0000000",
- "title": "Memory Allocated (MB)",
- "value": "3891"
- },
- {
- "name": "start_epoch",
- "plugin": "core",
- "raw_value": "1684839797.0000000",
- "title": "Job Start Time",
- "value": "2023-05-23 13:03:17"
- },
- {
- "name": "end_epoch",
- "plugin": "core",
- "raw_value": "1684839860.0000000",
- "title": "Job End Time",
- "value": "2023-05-23 13:04:20"
- },
- {
- "name": "runtime_seconds",
- "plugin": "core",
- "raw_value": "63.0000000",
- "title": "Job Runtime (Wall Clock)",
- "value": "1 minute"
- },
- {
- "name": "cpuacct.usage",
- "plugin": "cgroup",
- "raw_value": "17604876182.0000000",
- "title": "CPU Time",
- "value": "17.604876182 seconds"
- },
- {
- "name": "memory.failcnt",
- "plugin": "cgroup",
- "raw_value": "0E-7",
- "title": "Failed to allocate memory count",
- "value": 0.0
- },
- {
- "name": "memory.limit_in_bytes",
- "plugin": "cgroup",
- "raw_value": "12348030976.0000000",
- "title": "Memory limit on cgroup (MEM)",
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- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nsingle fastqs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\npaired fastqs\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nDrosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Cutadapt: remove bad quality bp\"];\n 0 -->|output| 3;\n 4[\"Flatten paired collection for FastQC\"];\n 1 -->|output| 4;\n 5[\"Cutadapt\"];\n 1 -->|output| 5;\n 6[\"Get gene length\"];\n 2 -->|output| 6;\n 077640cc-edbb-4185-9eb1-d11b522774af[\"Output\\nGene length\"];\n 6 --> 077640cc-edbb-4185-9eb1-d11b522774af;\n style 077640cc-edbb-4185-9eb1-d11b522774af stroke:#2c3143,stroke-width:4px;\n 7[\"convert gtf to bed12\"];\n 2 -->|output| 7;\n 8[\"STAR: map single reads\"];\n 2 -->|output| 8;\n 3 -->|out1| 8;\n 9[\"Merge fastqs for FastQC\"];\n 4 -->|output| 9;\n 0 -->|output| 9;\n 10[\"Merge Cutadapt reports\"];\n 5 -->|report| 10;\n 3 -->|report| 10;\n 11[\"STAR: map paired reads\"];\n 2 -->|output| 11;\n 5 -->|out_pairs| 11;\n 12[\"count reads per gene for SR\"];\n 8 -->|mapped_reads| 12;\n 2 -->|output| 12;\n 13[\"FastQC check read qualities\"];\n 9 -->|output| 13;\n 14[\"Combine cutadapt results\"];\n 10 -->|output| 14;\n cab760db-5c9d-4a3c-b768-998bfbac6b57[\"Output\\nmultiqc_cutadapt_html\"];\n 14 --> cab760db-5c9d-4a3c-b768-998bfbac6b57;\n style cab760db-5c9d-4a3c-b768-998bfbac6b57 stroke:#2c3143,stroke-width:4px;\n 15[\"Merge STAR logs\"];\n 11 -->|output_log| 15;\n 8 -->|output_log| 15;\n 16[\"Merge STAR counts\"];\n 8 -->|reads_per_gene| 16;\n 11 -->|reads_per_gene| 16;\n 17[\"count fragments per gene for PE\"];\n 11 -->|mapped_reads| 17;\n 2 -->|output| 17;\n 1527b5d7-1681-4934-9d9e-3a5f86ae0fee[\"Output\\nfeatureCounts_gene_length\"];\n 17 --> 1527b5d7-1681-4934-9d9e-3a5f86ae0fee;\n style 1527b5d7-1681-4934-9d9e-3a5f86ae0fee stroke:#2c3143,stroke-width:4px;\n 18[\"Merge STAR BAM\"];\n 11 -->|mapped_reads| 18;\n 8 -->|mapped_reads| 18;\n 802017f4-fb1a-4243-b50d-2ed46f746f11[\"Output\\nSTAR_BAM\"];\n 18 --> 802017f4-fb1a-4243-b50d-2ed46f746f11;\n style 802017f4-fb1a-4243-b50d-2ed46f746f11 stroke:#2c3143,stroke-width:4px;\n 19[\"merge coverage unique strand 1\"];\n 8 -->|signal_unique_str1| 19;\n 11 -->|signal_unique_str1| 19;\n 20[\"merge coverage unique strand 2\"];\n 8 -->|signal_unique_str2| 20;\n 11 -->|signal_unique_str2| 20;\n 21[\"Combine FastQC results\"];\n 13 -->|text_file| 21;\n 8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd[\"Output\\nmultiqc_fastqc_html\"];\n 21 --> 8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd;\n style 8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd stroke:#2c3143,stroke-width:4px;\n 22[\"Combine STAR Results\"];\n 15 -->|output| 22;\n 204e3f6c-6f54-46f0-b07c-1f31113265e7[\"Output\\nmultiqc_star_html\"];\n 22 --> 204e3f6c-6f54-46f0-b07c-1f31113265e7;\n style 204e3f6c-6f54-46f0-b07c-1f31113265e7 stroke:#2c3143,stroke-width:4px;\n 23[\"Remove statistics from STAR counts\"];\n 16 -->|output| 23;\n 24[\"Determine library strandness with STAR\"];\n 16 -->|output| 24;\n fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a[\"Output\\nmultiqc_star_counts_html\"];\n 24 --> fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a;\n style fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a stroke:#2c3143,stroke-width:4px;\n 25[\"merge counts from featureCounts\"];\n 12 -->|output_short| 25;\n 17 -->|output_short| 25;\n c82388f8-cb09-4fdf-8a0e-03cdad579f37[\"Output\\nfeatureCounts\"];\n 25 --> c82388f8-cb09-4fdf-8a0e-03cdad579f37;\n style c82388f8-cb09-4fdf-8a0e-03cdad579f37 stroke:#2c3143,stroke-width:4px;\n 26[\"merge featureCounts summary\"];\n 12 -->|output_summary| 26;\n 17 -->|output_summary| 26;\n 27[\"Determine library strandness with Infer Experiment\"];\n 18 -->|output| 27;\n 7 -->|bed_file| 27;\n 940ec3ec-dd2e-4d50-bbc4-756945eb16b2[\"Output\\ninferexperiment\"];\n 27 --> 940ec3ec-dd2e-4d50-bbc4-756945eb16b2;\n style 940ec3ec-dd2e-4d50-bbc4-756945eb16b2 stroke:#2c3143,stroke-width:4px;\n 28[\"Read Distribution\"];\n 18 -->|output| 28;\n 7 -->|bed_file| 28;\n 29[\"Compute read distribution statistics\"];\n 18 -->|output| 29;\n 7 -->|bed_file| 29;\n 30[\"sample BAM\"];\n 18 -->|output| 30;\n 31[\"Get reads number per chromosome\"];\n 18 -->|output| 31;\n 32[\"Remove duplicates\"];\n 18 -->|output| 32;\n 33[\"Determine library strandness with STAR coverage\"];\n 19 -->|output| 33;\n 20 -->|output| 33;\n 2 -->|output| 33;\n 89e1b053-03c2-467a-95a0-d2dc404670ec[\"Output\\npgt\"];\n 33 --> 89e1b053-03c2-467a-95a0-d2dc404670ec;\n style 89e1b053-03c2-467a-95a0-d2dc404670ec stroke:#2c3143,stroke-width:4px;\n 34[\"Select unstranded counts\"];\n 23 -->|outfile| 34;\n bce755be-ac3b-4346-9ac5-1128a287bf00[\"Output\\ncounts_from_star\"];\n 34 --> bce755be-ac3b-4346-9ac5-1128a287bf00;\n style bce755be-ac3b-4346-9ac5-1128a287bf00 stroke:#2c3143,stroke-width:4px;\n 35[\"Sort counts to get gene with highest count on feature Counts\"];\n 25 -->|output| 35;\n 6aeb4dd1-445f-4c66-b1ce-4bb8faac53db[\"Output\\nfeatureCounts_sorted\"];\n 35 --> 6aeb4dd1-445f-4c66-b1ce-4bb8faac53db;\n style 6aeb4dd1-445f-4c66-b1ce-4bb8faac53db stroke:#2c3143,stroke-width:4px;\n 36[\"Combine read asignments statistics\"];\n 26 -->|output| 36;\n fc72242a-f23c-4ceb-9a8b-5280343ea5d6[\"Output\\nmultiqc_featureCounts_html\"];\n 36 --> fc72242a-f23c-4ceb-9a8b-5280343ea5d6;\n style fc72242a-f23c-4ceb-9a8b-5280343ea5d6 stroke:#2c3143,stroke-width:4px;\n 37[\"Combine read distribution on known features\"];\n 29 -->|output| 37;\n 07dca732-0ac7-432e-9e61-2b77f921a23b[\"Output\\nmultiqc_read_distrib\"];\n 37 --> 07dca732-0ac7-432e-9e61-2b77f921a23b;\n style 07dca732-0ac7-432e-9e61-2b77f921a23b stroke:#2c3143,stroke-width:4px;\n 38[\"Get gene body coverage\"];\n 30 -->|outputsam| 38;\n 7 -->|bed_file| 38;\n 39[\"Combine results on reads per chromosome\"];\n 31 -->|output| 39;\n 7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf[\"Output\\nmultiqc_reads_per_chrom\"];\n 39 --> 7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf;\n style 7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf stroke:#2c3143,stroke-width:4px;\n 40[\"Combine results of duplicate reads\"];\n 32 -->|metrics_file| 40;\n 66553d0f-e851-458b-82c2-f9b30e394bac[\"Output\\nmultiqc_dup\"];\n 40 --> 66553d0f-e851-458b-82c2-f9b30e394bac;\n style 66553d0f-e851-458b-82c2-f9b30e394bac stroke:#2c3143,stroke-width:4px;\n 41[\"Sort counts to get gene with highest count on STAR\"];\n 34 -->|out_file1| 41;\n 383df008-0ccb-4d67-98dd-33fa5e2db81e[\"Output\\ncounts_from_star_sorted\"];\n 41 --> 383df008-0ccb-4d67-98dd-33fa5e2db81e;\n style 383df008-0ccb-4d67-98dd-33fa5e2db81e stroke:#2c3143,stroke-width:4px;\n 42[\"Combine gene body coverage\"];\n 38 -->|outputtxt| 42;\n 8544ea5c-faf2-44c9-85d6-40658fc9b9eb[\"Output\\nmultiqc_gene_body_cov\"];\n 42 --> 8544ea5c-faf2-44c9-85d6-40658fc9b9eb;\n style 8544ea5c-faf2-44c9-85d6-40658fc9b9eb stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-06-24 00:06:34 +0000",
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- "name": "Peter van Heusden"
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- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nPaired list collection with PE fastqs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nDrosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\ud83d\udee0\ufe0f Subworkflow\\nFastQC\"];\n style 2 fill:#edd,stroke:#900,stroke-width:4px;\n 0 -->|output| 2;\n 5f7652f1-e225-4ad1-8dbd-4d21544edb89[\"Output\\nmultiqc_fastqc_html\"];\n 2 --> 5f7652f1-e225-4ad1-8dbd-4d21544edb89;\n style 5f7652f1-e225-4ad1-8dbd-4d21544edb89 stroke:#2c3143,stroke-width:4px;\n 3[\"\ud83d\udee0\ufe0f Subworkflow\\ncutadapt\"];\n style 3 fill:#edd,stroke:#900,stroke-width:4px;\n 0 -->|output| 3;\n 41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee[\"Output\\nmultiqc_cutadapt_html\"];\n 3 --> 41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee;\n style 41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee stroke:#2c3143,stroke-width:4px;\n 4[\"\ud83d\udee0\ufe0f Subworkflow\\nSTAR + multiQC\"];\n style 4 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 4;\n 3 -->|out_pairs| 4;\n 8aa5ef30-3f09-4a93-944d-0d89101c056a[\"Output\\nmultiqc_star_html\"];\n 4 --> 8aa5ef30-3f09-4a93-944d-0d89101c056a;\n style 8aa5ef30-3f09-4a93-944d-0d89101c056a stroke:#2c3143,stroke-width:4px;\n 11af5c57-91b4-496c-9b0c-b02904963f81[\"Output\\nSTAR_BAM\"];\n 4 --> 11af5c57-91b4-496c-9b0c-b02904963f81;\n style 11af5c57-91b4-496c-9b0c-b02904963f81 stroke:#2c3143,stroke-width:4px;\n 5[\"\ud83d\udee0\ufe0f Subworkflow\\nmore QC\"];\n style 5 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 5;\n 4 -->|STAR_BAM| 5;\n b306cb12-a275-4c6d-b609-47fdc208864b[\"Output\\nmultiqc_reads_per_chrom_html\"];\n 5 --> b306cb12-a275-4c6d-b609-47fdc208864b;\n style b306cb12-a275-4c6d-b609-47fdc208864b stroke:#2c3143,stroke-width:4px;\n 3ea82568-5698-49a7-88fe-91381070aac2[\"Output\\nmultiqc_dup_html\"];\n 5 --> 3ea82568-5698-49a7-88fe-91381070aac2;\n style 3ea82568-5698-49a7-88fe-91381070aac2 stroke:#2c3143,stroke-width:4px;\n f2eed352-ca21-4d65-8810-f5a1d3c282b4[\"Output\\nmultiqc_read_distrib_html\"];\n 5 --> f2eed352-ca21-4d65-8810-f5a1d3c282b4;\n style f2eed352-ca21-4d65-8810-f5a1d3c282b4 stroke:#2c3143,stroke-width:4px;\n 3375d63c-cdc3-4fbb-8a55-6f504c934918[\"Output\\nmultiqc_gene_body_cov_html\"];\n 5 --> 3375d63c-cdc3-4fbb-8a55-6f504c934918;\n style 3375d63c-cdc3-4fbb-8a55-6f504c934918 stroke:#2c3143,stroke-width:4px;\n 6[\"\ud83d\udee0\ufe0f Subworkflow\\nDetermine strandness\"];\n style 6 fill:#edd,stroke:#900,stroke-width:4px;\n 4 -->|STAR_BAM| 6;\n 1 -->|output| 6;\n 4 -->|signal_unique_str1| 6;\n 4 -->|signal_unique_str2| 6;\n 4 -->|reads_per_gene| 6;\n 9727824a-3eb2-4430-92d1-b3c40c3041d1[\"Output\\npgt\"];\n 6 --> 9727824a-3eb2-4430-92d1-b3c40c3041d1;\n style 9727824a-3eb2-4430-92d1-b3c40c3041d1 stroke:#2c3143,stroke-width:4px;\n 105313d8-e31a-405d-8fcd-cc5fd93275e2[\"Output\\nmultiqc_star_counts_html\"];\n 6 --> 105313d8-e31a-405d-8fcd-cc5fd93275e2;\n style 105313d8-e31a-405d-8fcd-cc5fd93275e2 stroke:#2c3143,stroke-width:4px;\n fb810859-f2d0-43f8-ac7c-5c714c5c6805[\"Output\\ninferexperiment\"];\n 6 --> fb810859-f2d0-43f8-ac7c-5c714c5c6805;\n style fb810859-f2d0-43f8-ac7c-5c714c5c6805 stroke:#2c3143,stroke-width:4px;\n 7[\"\ud83d\udee0\ufe0f Subworkflow\\ncount STAR\"];\n style 7 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 7;\n 4 -->|reads_per_gene| 7;\n 7b7c698b-4808-4b45-adf1-686f8d273d18[\"Output\\nGene length\"];\n 7 --> 7b7c698b-4808-4b45-adf1-686f8d273d18;\n style 7b7c698b-4808-4b45-adf1-686f8d273d18 stroke:#2c3143,stroke-width:4px;\n bd3388e6-5b45-4fdc-9780-3efd1c34ebf8[\"Output\\ncounts_from_star_sorted\"];\n 7 --> bd3388e6-5b45-4fdc-9780-3efd1c34ebf8;\n style bd3388e6-5b45-4fdc-9780-3efd1c34ebf8 stroke:#2c3143,stroke-width:4px;\n 5fee8aff-4023-43f1-a653-f5af5357d798[\"Output\\ncounts_from_star\"];\n 7 --> 5fee8aff-4023-43f1-a653-f5af5357d798;\n style 5fee8aff-4023-43f1-a653-f5af5357d798 stroke:#2c3143,stroke-width:4px;\n 8[\"\ud83d\udee0\ufe0f Subworkflow\\ncount featureCount\"];\n style 8 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 8;\n 4 -->|STAR_BAM| 8;\n 46c7a2e8-7819-4715-a028-7ad1de9ed605[\"Output\\nfeatureCounts\"];\n 8 --> 46c7a2e8-7819-4715-a028-7ad1de9ed605;\n style 46c7a2e8-7819-4715-a028-7ad1de9ed605 stroke:#2c3143,stroke-width:4px;\n 152ba01e-d4f2-4227-8812-87648a1c19ea[\"Output\\nmultiqc_featureCounts_html\"];\n 8 --> 152ba01e-d4f2-4227-8812-87648a1c19ea;\n style 152ba01e-d4f2-4227-8812-87648a1c19ea stroke:#2c3143,stroke-width:4px;\n 8b9d6c76-6e82-4691-b8bc-9996d6ae1594[\"Output\\nfeatureCounts_gene_length\"];\n 8 --> 8b9d6c76-6e82-4691-b8bc-9996d6ae1594;\n style 8b9d6c76-6e82-4691-b8bc-9996d6ae1594 stroke:#2c3143,stroke-width:4px;\n f0de4714-4df8-4506-90d9-384537ad663e[\"Output\\nfeatureCounts_sorted\"];\n 8 --> f0de4714-4df8-4506-90d9-384537ad663e;\n style f0de4714-4df8-4506-90d9-384537ad663e stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-06-24 00:06:34 +0000",
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- "title": "QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows",
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- | adapter_removal | -adapter_removal | -Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. | -adapterremoval | -adapterremoval | -- | AdapterRemoval | -AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. | -Sequence trimming, Sequence merging, Primer removal | -- | Up-to-date | -https://github.com/MikkelSchubert/adapterremoval | -Fasta Manipulation, Sequence Analysis | -adapter_removal | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal | -2.3.3 | -adapterremoval | -2.3.3 | -Sequence trimming, Sequence merging, Primer removal | -- | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -37 | -217 | -- |
- | agat | -agat | -GTF/GFF analysis toolkit | -agat | -agat | -- | AGAT | -Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. | -Data handling, Genome annotation | -Genomics | -To update | -https://github.com/NBISweden/AGAT | -Convert Formats, Statistics, Fasta Manipulation | -agat | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/agat | -https://github.com/bgruening/galaxytools/tree/master/tools/agat | -1.2.0 | -agat | -1.4.0 | -Data handling, Genome annotation | -Genomics | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -42 | -481 | -- |
- | align_back_trans | -align_back_trans | -Thread nucleotides onto a protein alignment (back-translation) | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans | -Fasta Manipulation, Sequence Analysis | -align_back_trans | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans | -https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans | -0.0.10 | -biopython | -1.70 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -11 | -329 | -- |
- | assembly-stats | -assembly_stats | -Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. | -- | - | - | - | - | - | - | To update | -https://github.com/rjchallis/assembly-stats | -Assembly | -assembly_stats | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats | -17.02 | -rjchallis-assembly-stats | -- | - | - | 0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | assemblystats | -assemblystats | -Summarise an assembly (e.g. N50 metrics) | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools | -Assembly | -assemblystats | -nml | -https://github.com/phac-nml/galaxy_tools | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats | -1.1.0 | -perl-bioperl | -1.7.8 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | atactk_trim_adapters | -atactk_trim_adapters | -Trim adapters from paired-end HTS reads. | -- | - | - | - | - | - | - | To update | -https://github.com/ParkerLab/atactk/ | -Fastq Manipulation | -atactk_trim_adapters | -rnateam | -https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters | -https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters | -0.1.6 | -atactk | -0.1.9 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -26 | -257 | -- |
- | bam2mappingstats | -bam2mappingstats | -Generates mapping stats from a bam file. | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools | -Assembly | -bam2mappingstats | -nml | -https://github.com/phac-nml/galaxy_tools | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats | -1.1.0 | -perl | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | barcode_splitter | -barcode_splitter | -A utility to split sequence files using multiple sets of barcodes | -- | - | - | - | - | - | - | To update | -https://bitbucket.org/princeton_genomics/barcode_splitter/ | -Fastq Manipulation | -barcode_splitter | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter | -0.18.4.0 | -barcode_splitter | -0.18.6 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | berokka | -berokka | -Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. | -- | - | - | - | - | - | - | To update | -https://github.com/tseemann/berokka | -Fasta Manipulation | -berokka | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka | -0.2.3 | -berokka | -- | - | - | 0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | bionano | -bionano_scaffold | -Bionano Solve is a set of tools for analyzing Bionano data | -- | - | - | - | - | - | - | To update | -https://bionanogenomics.com/ | -Assembly | -bionano | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/bionano | -https://github.com/bgruening/galaxytools/tree/master/tools/bionano | -3.7.0 | -- | - | - | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -112 | -531 | -- |
- | biscot | -biscot | -Bionano scaffolding correction tool | -- | - | - | - | - | - | - | To update | -https://github.com/institut-de-genomique/biscot | -Assembly | -biscot | -iuc | -https://github.com/bgruening/iuc/tree/master/tools/biscot | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot | -2.3.3 | -biscot | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -3 | -- |
- | blast_rbh | -blast_reciprocal_best_hits | -BLAST Reciprocal Best Hits (RBH) from two FASTA files | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | -Fasta Manipulation, Sequence Analysis | -blast_rbh | -peterjc | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | -0.3.0 | -biopython | -1.70 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -121 | -22499 | -- |
- | blast_to_scaffold | -blast2scaffold | -Generate DNA scaffold from blastn or tblastx alignments of Contigs | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -RNA, Sequence Analysis, Assembly | -blast_to_scaffold | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold | -1.1.0 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | blast_unmatched | -blast_unmatched | -Extract unmatched query sequences from blast | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Fasta Manipulation | -blast_unmatched | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched | -1.0.1 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | blastparser_and_hits | -BlastParser_and_hits | -Parse blast outputs and compile hits | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Assembly, RNA | -blastparser_and_hits | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits | -2.7.1 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | blastx_to_scaffold | -blastx2scaffold | -Generate DNA scaffold from blastx alignment of Contigs | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -RNA, Sequence Analysis, Assembly | -blastx_to_scaffold | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold | -1.1.1 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | blobtoolkit | -blobtoolkit | -Identification and isolation non-target data in draft and publicly available genome assemblies. | -- | - | - | - | - | - | - | To update | -https://blobtoolkit.genomehubs.org/ | -Sequence Analysis, Assembly | -blobtoolkit | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit | -https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit | -4.0.7 | -- | - | - | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -21 | -685 | -- |
- | cap3 | -cap3 | -cap3 wrapper | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Assembly | -cap3 | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 | -https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 | -2.0.1 | -cap3 | -10.2011 | -- | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -101 | -7766 | -- |
- | cdhit | -cd_hit | -Cluster or compare biological sequence datasets | -cd-hit | -cd-hit | -- | cd-hit | -Cluster a nucleotide dataset into representative sequences. | -Sequence clustering | -Sequencing | -Up-to-date | -http://weizhongli-lab.org/cd-hit/ | -Sequence Analysis, Fasta Manipulation | -cd_hit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit | -4.8.1 | -cd-hit | -4.8.1 | -Sequence clustering | -Sequencing | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -280 | -4474 | -- |
- | cherry_pick_fasta | -cherry_pick_fasta | -Pick fasta sequence with specific header content | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Fasta Manipulation | -cherry_pick_fasta | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta | -https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta | -4.1 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | circexplorer2 | -circexplorer2 | -Comprehensive and integrative circular RNA analysis toolset. | -circexplorer2 | -circexplorer2 | -- | CIRCexplorer2 | -Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. | -- | RNA splicing, Gene transcripts, Literature and language | -Up-to-date | -https://github.com/YangLab/CIRCexplorer2 | -RNA, Assembly | -circexplorer2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 | -2.3.8 | -circexplorer2 | -2.3.8 | -- | RNA splicing, Gene transcripts, Literature and language | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -16 | -269 | -- |
- | clc_assembly_cell | -clc_assembler, clc_mapper | -Galaxy wrapper for the CLC Assembly Cell suite from CLCBio | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell | -Assembly, Next Gen Mappers, SAM | -clc_assembly_cell | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell | -https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell | -0.0.7 | -samtools | -1.20 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | combine_assembly_stats | -combine_stats | -Combine multiple Assemblystats datasets into a single tabular report | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools | -Assembly | -combine_assemblystats | -nml | -https://github.com/phac-nml/galaxy_tools | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats | -1.0 | -perl-getopt-long | -2.58 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | convert_solid_color2nuc | -color2nuc | -Convert Color Space to Nucleotides | -- | - | - | - | - | - | - | To update | -- | Fasta Manipulation | -convert_solid_color2nuc | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc | -1.0.0 | -- | - | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | count_roi_variants | -count_roi_variants | -Count sequence variants in region of interest in BAM file | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants | -Assembly, SAM | -count_roi_variants | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants | -https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants | -0.0.6 | -samtools | -1.20 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | coverage_stats | -coverage_stats | -BAM coverage statistics using samtools idxstats and depth | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats | -Assembly, SAM | -coverage_stats | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats | -https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats | -0.1.0 | -samtools | -1.20 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | cutadapt | -cutadapt | -Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). | -cutadapt | -cutadapt | -- | Cutadapt | -Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. | -Sequence trimming, Primer removal, Read pre-processing | -Genomics, Probes and primers, Sequencing | -To update | -https://cutadapt.readthedocs.org/en/stable/ | -Fasta Manipulation, Fastq Manipulation, Sequence Analysis | -cutadapt | -lparsons | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt | -4.8 | -cutadapt | -4.9 | -Sequence trimming, Primer removal, Read pre-processing | -Genomics, Probes and primers, Sequencing | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -1 | -5090 | -232004 | -- |
- | disco | -disco | -DISCO is a overlap-layout-consensus (OLC) metagenome assembler | -disco | -disco | -- | DISCO | -DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. | -Protein sequence analysis | -Structure determination | -To update | -http://disco.omicsbio.org/ | -Metagenomics, Assembly | -disco | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco | -- | disco | -1.2 | -Protein sequence analysis | -Structure determination | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -42 | -369 | -- |
- | ear | -make_ear | -A tool to compile assembly reports and stastics from assembly pipeline | -- | - | - | - | - | - | - | To update | -https://github.com/ERGA-consortium/EARs/tree/main | -Sequence Analysis, Assembly | -erga_ear | -iuc | -https://github.com/ERGA-consortium/EARs/tree/main | -https://github.com/bgruening/galaxytools/tree/master/tools/ear | -1.0.0 | -reportlab | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | emboss_5 | -EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 | -Galaxy wrappers for EMBOSS version 5.0.0 tools | -emboss | -emboss | -- | EMBOSS | -Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. | -Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment | -Molecular biology, Sequence analysis, Biology | -To update | -http://emboss.open-bio.org/ | -Sequence Analysis, Fasta Manipulation | -emboss_5 | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 | -5.0.0 | -emboss | -6.6.0 | -Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment | -Molecular biology, Sequence analysis | -107 | -107 | -107 | -107 | -107 | -107 | -107 | -107 | -0 | -0 | -0 | -0 | -0 | -0 | -107 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -107 | -0 | -0 | -107 | -0 | -0 | -0 | -107 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -107 | -107 | -1816 | -89530 | -- |
- | fasplit | -fasplit | -faSplit is a tool to split a single FASTA file into several files | -UCSC_Genome_Browser_Utilities | -UCSC_Genome_Browser_Utilities | -- | UCSC Genome Browser Utilities | -Utilities for handling sequences and assemblies from the UCSC Genome Browser project. | -- | Sequence analysis | -Up-to-date | -http://hgdownload.cse.ucsc.edu/admin/exe/ | -Fasta Manipulation | -ucsc_fasplit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit | -377 | -ucsc-fasplit | -377 | -- | Sequence analysis | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -242 | -2644 | -- |
- | fasta_clipping_histogram | -cshl_fasta_clipping_histogram | -Length Distribution chart | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Graphics, Statistics | -fasta_clipping_histogram | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | fasta_compute_length | -fasta_compute_length | -Compute sequence length | -- | - | - | - | - | - | - | To update | -- | Fasta Manipulation | -fasta_compute_length | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length | -1.0.3 | -python | -- | - | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -380 | -7758 | -- |
- | fasta_concatenate_by_species | -fasta_concatenate0 | -Concatenate FASTA alignment by species | -- | - | - | - | - | - | - | To update | -- | Fasta Manipulation | -fasta_concatenate_by_species | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species | -0.0.1 | -bx-python | -0.11.0 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -88 | -35793 | -- |
- | fasta_filter_by_id | -fasta_filter_by_id | -Filter FASTA sequences by ID (DEPRECATED) | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id | -Fasta Manipulation, Sequence Analysis, Text Manipulation | -fasta_filter_by_id | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id | -0.0.7 | -galaxy_sequence_utils | -1.1.5 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | fasta_filter_by_length | -fasta_filter_by_length | -Filter sequences by length | -- | - | - | - | - | - | - | To update | -- | Fasta Manipulation | -fasta_filter_by_length | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length | -1.2 | -python | -- | - | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -350 | -48649 | -- |
- | fasta_formatter | -cshl_fasta_formatter | -FASTA Width formatter | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation | -fasta_formatter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -68 | -2912 | -- |
- | fasta_merge_files_and_filter_unique_sequences | -fasta_merge_files_and_filter_unique_sequences | -Concatenate FASTA database files together | -- | - | - | - | - | - | - | To update | -https://github.com/galaxyproteomics/tools-galaxyp/ | -Fasta Manipulation | -fasta_merge_files_and_filter_unique_sequences | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences | -1.2.0 | -python | -- | - | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -461 | -29886 | -- |
- | fasta_nucleotide_changer | -cshl_fasta_nucleotides_changer | -RNA/DNA converter. | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation | -fasta_nucleotide_changer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -29 | -774 | -- |
- | fasta_to_tabular | -fasta2tab | -FASTA-to-Tabular converter | -- | - | - | - | - | - | - | To update | -- | Fasta Manipulation | -fasta_to_tabular | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular | -1.1.1 | -python | -- | - | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -622 | -105935 | -- |
- | fastk | -fastk_fastk | -FastK: A K-mer counter (for HQ assembly data sets) | -- | - | - | - | - | - | - | To update | -https://github.com/thegenemyers/FASTK | -Assembly | -fastk | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk | -1.0.0 | -fastk | -1.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | fastq_combiner | -fastq_combiner | -Combine FASTA and QUAL into FASTQ | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation, Fasta Manipulation | -fastq_combiner | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -66 | -8676 | -- |
- | fastq_filter | -fastq_filter | -Filter FASTQ reads by quality score and length | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_filter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -266 | -14222 | -- |
- | fastq_filter_by_id | -fastq_filter_by_id | -Filter FASTQ sequences by ID (DEPRECATED) | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id | -Fastq Manipulation, Sequence Analysis, Text Manipulation | -fastq_filter_by_id | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id | -0.0.7 | -galaxy_sequence_utils | -1.1.5 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | fastq_groomer | -fastq_groomer | -Convert between various FASTQ quality formats. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_groomer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1028 | -94802 | -- |
- | fastq_info | -fastq_info | -FASTQ info allows to validate single or paired fastq files | -- | - | - | - | - | - | - | To update | -https://github.com/nunofonseca/fastq_utils | -Fastq Manipulation | -fastq_info | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info | -https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info | -0.25.1 | -fastq_utils | -0.25.2 | -- | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -679 | -5765 | -- |
- | fastq_manipulation | -fastq_manipulation | -Manipulate FASTQ reads on various attributes. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_manipulation | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -69 | -2503 | -- |
- | fastq_masker_by_quality | -fastq_masker_by_quality | -FASTQ Masker by quality score | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_masker_by_quality | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -16 | -170 | -- |
- | fastq_pair | -fastq_pair | -Paired-end fastq pairer | -- | - | - | - | - | - | - | To update | -https://github.com/linsalrob/fastq-pair | -Fastq Manipulation | -fastq_pair | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair | -1.0+galaxy0 | -fastq-pair | -1.0 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | fastq_paired_end_deinterlacer | -fastq_paired_end_deinterlacer | -FASTQ de-interlacer on paired end reads. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_paired_end_deinterlacer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -122 | -8410 | -- |
- | fastq_paired_end_interlacer | -fastq_paired_end_interlacer | -FASTQ interlacer on paired end reads | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_paired_end_interlacer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1087 | -17024 | -- |
- | fastq_paired_end_joiner | -fastq_paired_end_joiner | -FASTQ joiner on paired end reads | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_paired_end_joiner | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -245 | -16635 | -- |
- | fastq_paired_end_splitter | -fastq_paired_end_splitter | -FASTQ splitter on joined paired end reads | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_paired_end_splitter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -196 | -3092 | -- |
- | fastq_quality_boxplot | -cshl_fastq_quality_boxplot | -Draw quality score boxplot | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation, Graphics, Statistics | -fastq_quality_boxplot | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -51 | -1178 | -- |
- | fastq_quality_converter | -cshl_fastq_quality_converter | -Quality format converter (ASCII-Numeric) | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation | -fastq_quality_converter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -11 | -220 | -- |
- | fastq_quality_filter | -cshl_fastq_quality_filter | -Filter by quality | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation | -fastq_quality_filter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1509 | -15172 | -- |
- | fastq_quality_trimmer | -cshl_fastq_quality_trimmer | -FASTQ trimmer based on quality | -- | - | - | - | - | - | - | To update | -https://github.com/agordon/fastx_toolkit | -Fastq Manipulation | -fastq_quality_trimmer | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer | -0.0.14+galaxy0 | -fastx_toolkit | -0.0.14 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | fastq_stats | -fastq_stats | -FASTQ Summary Statistics by column | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_stats | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -221 | -4246 | -- |
- | fastq_to_fasta | -cshl_fastq_to_fasta | -FASTQ to FASTA converter | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Convert Formats | -fastq_to_fasta | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -419 | -13599 | -- |
- | fastq_to_tabular | -fastq_to_tabular | -FASTQ to Tabular converter | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_to_tabular | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -93 | -12593 | -- |
- | fastq_trimmer | -fastq_trimmer | -FASTQ Trimmer by quality | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_trimmer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -210 | -9757 | -- |
- | fastq_trimmer_by_quality | -fastq_quality_trimmer | -FASTQ Quality Trimmer by sliding window | -- | - | - | - | - | - | - | Up-to-date | -- | Fastq Manipulation | -fastq_trimmer_by_quality | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -459 | -5676 | -- |
- | fastqc | -fastqc | -Read QC reports using FastQC | -fastqc | -fastqc | -- | FastQC | -This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. | -Sequence composition calculation, Sequencing quality control, Statistical calculation | -Sequencing, Data quality management, Sequence analysis | -To update | -http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | -Fastq Manipulation | -fastqc | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc | -0.74+galaxy0 | -fastqc | -0.12.1 | -Sequence composition calculation, Sequencing quality control, Statistical calculation | -Sequencing, Data quality management, Sequence analysis | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -1 | -17447 | -1556625 | -- |
- | fastqsolexa_to_fasta_qual | -fastqsolexa_to_fasta_qual | -FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data | -- | - | - | - | - | - | - | To update | -- | Convert Formats, Fastq Manipulation | -fastqsolexa_to_fasta_qual | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual | -1.0.0 | -- | - | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | fastqtofasta | -fastq_to_fasta_python | -FASTQ to FASTA converter | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastqtofasta | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1371 | -178178 | -- |
- | fastx_artifacts_filter | -cshl_fastx_artifacts_filter | -Remove sequencing artifacts | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Fastq Manipulation | -fastx_artifacts_filter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -27 | -1810 | -- |
- | fastx_barcode_splitter | -cshl_fastx_barcode_splitter | -Barcode Splitter | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Fastq Manipulation | -fastx_barcode_splitter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -128 | -16591 | -- |
- | fastx_clipper | -cshl_fastx_clipper | -Clip adapter sequences | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Fastq Manipulation | -fastx_clipper | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -96 | -3333 | -- |
- | fastx_collapser | -cshl_fastx_collapser | -Collapse sequences | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation | -fastx_collapser | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -114 | -61218 | -- |
- | fastx_nucleotides_distribution | -cshl_fastx_nucleotides_distribution | -Draw nucleotides distribution chart | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation, Graphics | -fastx_nucleotides_distribution | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -25 | -249 | -- |
- | fastx_quality_statistics | -cshl_fastx_quality_statistics | -Compute quality statistics | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation, Statistics | -fastx_quality_statistics | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -63 | -2176 | -- |
- | fastx_renamer | -cshl_fastx_renamer | -Rename sequences | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Fastq Manipulation | -fastx_renamer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -68 | -2280 | -- |
- | fastx_reverse_complement | -cshl_fastx_reverse_complement | -Reverse-Complement | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation, Fasta Manipulation | -fastx_reverse_complement | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -156 | -10832 | -- |
- | fastx_trimmer | -cshl_fastx_trimmer | -Trim sequences | -- | - | - | - | - | - | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Fastq Manipulation | -fastx_trimmer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer | -0.0.14 | -fastx_toolkit | -0.0.14 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -205 | -13149 | -- |
- | fermikit | -fermi2, fermikit_variants | -FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/lh3/fermikit | -Assembly, Variant Analysis | -fermikit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit | -r193 | -fermi2 | -r193 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | fetch_fasta_from_ncbi | -retrieve_fasta_from_NCBI | -Fetch fasta sequences from NCBI using eutils wrappers | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Fasta Manipulation, Data Source | -fetch_fasta_from_ncbi | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi | -https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi | -3.1.0 | -urllib3 | -1.12 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | filter_by_fasta_ids | -filter_by_fasta_ids | -Filter FASTA on the headers and/or the sequences | -- | - | - | - | - | - | - | To update | -- | Fasta Manipulation, Proteomics | -filter_by_fasta_ids | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids | -2.3 | -python | -- | - | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -426 | -26274 | -- |
- | filter_spades_repeats | -filter_spades_repeat | -Remove short and repeat contigs/scaffolds | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools/ | -Assembly | -filter_spades_repeats | -nml | -https://github.com/phac-nml/galaxy_tools/ | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats | -1.0.1 | -perl-bioperl | -1.7.8 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | filtlong | -filtlong | -Filtlong - Filtering long reads by quality | -filtlong | -filtlong | -- | Filtlong | -Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. | -Filtering, Sequencing quality control | -- | Up-to-date | -https://github.com/rrwick/Filtlong | -Fastq Manipulation, Sequence Analysis | -filtlong | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong | -0.2.1 | -filtlong | -0.2.1 | -Filtering, Sequencing quality control | -- | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -617 | -30483 | -- |
- | flair | -flair_collapse, flair_correct | -FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. | -- | - | - | - | - | - | - | To update | -https://github.com/BrooksLabUCSC/flair | -Nanopore | -flair | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair | -1.5 | -flair | -2.0.0 | -- | - | 0 | -0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -14 | -331 | -- |
- | flash | -flash | -Fast Length Adjustment of SHort reads | -flash | -flash | -- | FLASH | -Identifies paired-end reads which overlap in the middle, converting them to single long reads | -Read pre-processing, Sequence merging, Sequence assembly | -Sequencing, Sequence assembly | -Up-to-date | -https://ccb.jhu.edu/software/FLASH/ | -Assembly, Fastq Manipulation | -flash | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash | -1.2.11 | -flash | -1.2.11 | -Read pre-processing, Sequence merging, Sequence assembly | -Sequencing, Sequence assembly | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -74 | -13759 | -- |
- | flye | -flye | -Assembly of long and error-prone reads. | -Flye | -Flye | -- | Flye | -Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. | -Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly | -Sequence assembly, Metagenomics, Whole genome sequencing, Genomics | -To update | -https://github.com/fenderglass/Flye/ | -Assembly | -flye | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/flye | -https://github.com/bgruening/galaxytools/tree/master/tools/flye | -2.9.3 | -flye | -2.9.4 | -Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly | -Sequence assembly, Metagenomics, Whole genome sequencing | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1499 | -20904 | -- |
- | format_cd_hit_output | -format_cd_hit_output | -Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file | -- | - | - | - | - | - | - | To update | -- | Fasta Manipulation | -format_cd_hit_output | -bebatut | -https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ | -https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output | -1.0.0+galaxy1 | -- | - | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -20 | -166 | -- |
- | get_pairs | -get_pairs | -Separate paired and unpaired reads from two fastq files | -- | - | - | - | - | - | - | To update | -- | Fastq Manipulation | -get_pairs | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs | -https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs | -0.3 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | get_reference_fasta | -get_fasta_reference | -Obtain reference genome sequence. | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Data Source, Fasta Manipulation | -get_reference_fasta | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta | -https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta | -0.3.2 | -- | - | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | getorganelle | -get_annotated_regions_from_gb, get_organelle_from_reads | -GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. | -getorganelle | -getorganelle | -- | GetOrganelle | -A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. | -De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming | -Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms | -Up-to-date | -https://github.com/Kinggerm/GetOrganelle | -Assembly | -getorganelle | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle | -1.7.7.1 | -getorganelle | -1.7.7.1 | -De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming | -Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms | -0 | -2 | -2 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -18 | -495 | -- |
- | graphmap | -graphmap_align, graphmap_overlap | -Mapper for long, error-prone reads. | -graphmap | -graphmap | -- | graphmap | -Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 | -Sequence trimming, EST assembly, Read mapping | -Gene transcripts, RNA-Seq, RNA splicing | -To update | -https://github.com/isovic/graphmap/ | -Assembly | -graphmap | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/graphmap | -https://github.com/bgruening/galaxytools/tree/master/tools/graphmap | -0.5.2 | -graphmap | -0.6.3 | -Sequence trimming, EST assembly, Read mapping | -Gene transcripts, RNA-Seq, RNA splicing | -0 | -0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -136 | -6651 | -- |
- | guppy | -guppy-basecaller | -A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Nanopore | -guppy_basecaller | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy | -https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy | -0.2.2 | -- | - | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | hapcut2 | -hapcut2 | -Robust and accurate haplotype assembly for diverse sequencing technologies | -hapcut2 | -hapcut2 | -- | HapCUT2 | -HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md | -Haplotype mapping, Variant classification | -- | Up-to-date | -https://github.com/vibansal/HapCUT2 | -Assembly | -hapcut2 | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 | -1.3.4 | -hapcut2 | -1.3.4 | -Haplotype mapping, Variant classification | -- | 0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | hapog | -hapog | -Hapo-G - Haplotype-Aware Polishing of Genomes | -hapog | -hapog | -- | Hapo-G | -Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. | -Genome assembly, Optimisation and refinement | -Sequence assembly, Genomics | -Up-to-date | -https://github.com/institut-de-genomique/HAPO-G | -Assembly | -hapog | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog | -1.3.8 | -hapog | -1.3.8 | -Genome assembly, Optimisation and refinement | -Sequence assembly, Genomics | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -36 | -295 | -- |
- | hifiasm | -hifiasm | -A fast haplotype-resolved de novo assembler | -- | - | - | - | - | - | - | To update | -https://github.com/chhylp123/hifiasm | -Assembly | -hifiasm | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm | -https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm | -0.19.8 | -hifiasm | -0.19.9 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -297 | -1410 | -- |
- | hisat | -hisat | -HISAT is a fast and sensitive spliced alignment program. | -- | - | - | - | - | - | - | To update | -http://ccb.jhu.edu/software/hisat/index.shtml | -Assembly | -hisat | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat | -1.0.3 | -hisat | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -228 | -- |
- | hisat2 | -hisat2 | -HISAT2 is a fast and sensitive spliced alignment program. | -hisat2 | -hisat2 | -- | HISAT2 | -Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). | -Sequence alignment | -RNA-seq | -Up-to-date | -http://ccb.jhu.edu/software/hisat2/ | -Assembly | -hisat2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 | -2.2.1 | -hisat2 | -2.2.1 | -Sequence alignment | -- | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -4183 | -299104 | -- |
- | hypo | -hypo | -Super Fast & Accurate Polisher for Long Read Genome Assemblies | -HyPo | -HyPo | -- | HyPo | -HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. | -Optimisation and refinement, Genome assembly | -Sequence assembly, Genomics | -Up-to-date | -https://github.com/kensung-lab/hypo | -Assembly | -hypo | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo | -1.0.3 | -hypo | -1.0.3 | -Optimisation and refinement, Genome assembly | -Sequence assembly, Genomics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -39 | -354 | -- |
- | idba_ud | -idba_hybrid, idba_tran, idba_ud | -Wrappers for the idba assembler variants. | -idba | -idba | -- | IDBA | -A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. | -Sequence assembly | -Sequence assembly | -To update | -https://i.cs.hku.hk/~alse/hkubrg/projects/index.html | -Assembly | -idba | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud | -- | idba | -1.1.3 | -Sequence assembly | -Sequence assembly | -3 | -0 | -3 | -3 | -3 | -0 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -69 | -1127 | -- |
- | instagraal | -instagraal | -Large genome reassembly based on Hi-C data | -instagraal | -instagraal | -- | instaGRAAL | -Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) | -Genome assembly, Mapping assembly, Genetic mapping, Scaffolding | -Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites | -To update | -https://github.com/koszullab/instaGRAAL | -Assembly | -instagraal | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/instagraal | -https://github.com/bgruening/galaxytools/tree/master/tools/instagraal | -0.1.6 | -- | - | Genome assembly, Mapping assembly, Genetic mapping, Scaffolding | -Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -14 | -139 | -- |
- | jellyfish | -jellyfish | -Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA | -Jellyfish | -Jellyfish | -- | Jellyfish | -A command-line algorithm for counting k-mers in DNA sequence. | -k-mer counting | -Sequence analysis, Genomics | -To update | -https://github.com/gmarcais/Jellyfish | -Assembly | -jellyfish | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish | -- | kmer-jellyfish | -2.3.1 | -k-mer counting | -Sequence analysis, Genomics | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -91 | -1138 | -- |
- | khmer | -khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median | -In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more | -khmer | -khmer | -- | khmer | -khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. | -Standardisation and normalisation, De-novo assembly | -Sequence assembly | -Up-to-date | -https://khmer.readthedocs.org/ | -Assembly, Next Gen Mappers | -khmer | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer | -3.0.0a3 | -khmer | -3.0.0a3 | -Standardisation and normalisation, De-novo assembly | -Sequence assembly | -8 | -8 | -8 | -0 | -8 | -8 | -8 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -8 | -8 | -63 | -2022 | -- |
- | length_and_gc_content | -length_and_gc_content | -Gets gene length and gc content from a fasta and a GTF file | -- | - | - | - | - | - | - | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content | -Fasta Manipulation, Statistics, RNA, Micro-array Analysis | -length_and_gc_content | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content | -0.1.2 | -r-optparse | -1.3.2 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -322 | -4090 | -- |
- | lighter | -lighter | -Lighter is a kmer-based error correction method for whole genome sequencing data | -lighter | -lighter | -- | Lighter | -Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. | -k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection | -Sequencing, Whole genome sequencing, DNA, Genomics | -To update | -https://github.com/mourisl/Lighter | -Sequence Analysis, Fasta Manipulation | -lighter | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/lighter | -https://github.com/bgruening/galaxytools/tree/master/tools/lighter | -1.0 | -lighter | -1.1.3 | -k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection | -Whole genome sequencing, DNA, Genomics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -9 | -152 | -- |
- | links | -links | -Scaffold genome assemblies with long reads. | -links | -links | -- | LINKS | -LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. | -Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming | -Sequence assembly, Mapping, Sequencing | -Up-to-date | -https://github.com/bcgsc/LINKS | -Assembly | -links | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/links | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/links | -2.0.1 | -links | -2.0.1 | -Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming | -Sequence assembly, Mapping, Sequencing | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -77 | -405 | -- |
- | make_nr | -make_nr | -Make a FASTA file non-redundant | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr | -Fasta Manipulation, Sequence Analysis | -make_nr | -peterjc | -https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr | -https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr | -0.0.3 | -biopython | -1.70 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | megahit | -megahit | -An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. | -megahit | -megahit | -- | MEGAHIT | -Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. | -Genome assembly | -Metagenomics, Sequencing, Ecology, Sequence assembly | -Up-to-date | -https://github.com/voutcn/megahit | -Sequence Analysis, Assembly, Metagenomics | -megahit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit | -1.2.9 | -megahit | -1.2.9 | -Genome assembly | -Metagenomics, Sequencing, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -1 | -548 | -9530 | -- |
- | megahit_contig2fastg | -megahit_contig2fastg | -A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) | -megahit | -megahit | -- | MEGAHIT | -Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. | -Genome assembly | -Metagenomics, Sequencing, Ecology, Sequence assembly | -To update | -https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp | -Sequence Analysis, Assembly, Metagenomics | -megahit_contig2fastg | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg | -1.1.3 | -megahit | -1.2.9 | -Genome assembly | -Metagenomics, Sequencing, Sequence assembly | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -54 | -475 | -- |
- | merqury | -merqury, merquryplot | -Merqury is a tool for evaluating genomes assemblies based of k-mer operations. | -merqury | -merqury | -- | Merqury | -Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. | -Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly | -Sequence assembly, Whole genome sequencing, Plant biology | -Up-to-date | -https://github.com/marbl/merqury | -Assembly | -merqury | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury | -1.3 | -merqury | -1.3 | -Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly | -Sequence assembly, Whole genome sequencing, Plant biology | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -244 | -2483 | -- |
- | meryl | -meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode | -Meryl a k-mer counter. | -meryl | -meryl | -- | Meryl | -Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. | -k-mer counting | -Whole genome sequencing, Genomics, Sequence analysis, Sequencing | -Up-to-date | -https://github.com/marbl/meryl | -Assembly | -meryl | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl | -1.3 | -merqury | -1.3 | -k-mer counting | -Whole genome sequencing, Genomics, Sequence analysis | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | mgnify_seqprep | -mgnify_seqprep | -A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. | -seqprep | -seqprep | -- | SeqPrep | -Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. | -Nucleic acid design | -Genomics, Sequence assembly, Sequencing, Probes and primers | -To update | -https://github.com/jstjohn/SeqPrep | -Fastq Manipulation, Sequence Analysis | -mgnify_seqprep | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep | -https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep | -1.2 | -- | - | Nucleic acid design | -Genomics, Sequence assembly, Sequencing, Probes and primers | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | minia | -minia | -Short-read assembler based on a de Bruijn graph | -minia | -minia | -- | Minia | -Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | -Genome assembly | -Sequence assembly | -Up-to-date | -https://gatb.inria.fr/software/minia/ | -Assembly | -minia | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia | -3.2.6 | -minia | -3.2.6 | -Genome assembly | -Sequence assembly | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -109 | -2206 | -- |
- | miniasm | -miniasm | -Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) | -miniasm | -miniasm | -- | miniasm | -Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. | -De-novo assembly | -Genomics, Sequence assembly | -To update | -https://github.com/lh3/miniasm | -Assembly | -miniasm | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm | -0.3_r179 | -miniasm | -0.3 | -De-novo assembly | -Genomics, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -178 | -11938 | -- |
- | mitobim | -mitobim | -assemble mitochondrial genomes | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/chrishah/MITObim | -Assembly | -mitobim | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim | -1.9.1 | -mitobim | -1.9.1 | -- | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -66 | -881 | -- |
- | mitohifi | -mitohifi | -Assembly mitogenomes from Pacbio HiFi read. | -- | - | - | - | - | - | - | To update | -https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 | -Assembly | -mitohifi | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi | -https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi | -3 | -- | - | - | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -56 | -613 | -- |
- | msaboot | -msaboot | -A multiple sequences alignment bootstrapping tool. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/phac-nml/msaboot | -Fasta Manipulation | -msaboot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot | -0.1.2 | -msaboot | -0.1.2 | -- | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -34 | -803 | -- |
- | multiqc | -multiqc | -MultiQC aggregates results from bioinformatics analyses across many samples into a single report | -multiqc | -multiqc | -- | MultiQC | -MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. | -Validation, Sequencing quality control | -Sequencing, Bioinformatics, Sequence analysis, Genomics | -To update | -http://multiqc.info/ | -Fastq Manipulation, Statistics, Visualization | -multiqc | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc | -1.11 | -multiqc | -1.22.3 | -Sequencing quality control | -Sequencing, Bioinformatics, Sequence analysis, Genomics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -1 | -8320 | -162790 | -- |
- | necat | -necat | -Error correction and de-novo assembly for ONT Nanopore reads | -necat | -necat | -- | NECAT | -NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. | -De-novo assembly | -Sequence assembly | -Up-to-date | -https://github.com/xiaochuanle/NECAT | -Assembly | -necat | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat | -0.0.1_update20200803 | -necat | -0.0.1_update20200803 | -De-novo assembly | -Sequence assembly | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -95 | -667 | -- |
- | nextdenovo | -nextdenovo | -String graph-based de novo assembler for long reads | -nextdenovo | -nextdenovo | -- | NextDenovo | -NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. | -De-novo assembly, Genome assembly | -Sequencing, Sequence assembly | -To update | -https://github.com/Nextomics/NextDenovo | -Assembly | -nextdenovo | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo | -https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo | -2.5.0 | -nextdenovo | -2.5.2 | -De-novo assembly, Genome assembly | -Sequencing, Sequence assembly | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -84 | -268 | -- |
- | nlstradamus | -nlstradamus | -Find nuclear localization signals (NLSs) in protein sequences | -- | - | - | - | - | - | - | To update | -http://www.moseslab.csb.utoronto.ca/NLStradamus | -Fasta Manipulation, Sequence Analysis | -nlstradamus | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus | -https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus | -0.0.11 | -NLStradamus | -1.8 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | novoplasty | -novoplasty | -NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. | -- | - | - | - | - | - | - | To update | -https://github.com/ndierckx/NOVOPlasty | -Assembly | -novoplasty | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty | -4.3.1 | -novoplasty | -4.3.5 | -- | - | 0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -162 | -6384 | -- |
- | oases | -oasesoptimiserv | -Short read assembler | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Assembly, RNA | -oases | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/oases | -https://github.com/ARTbio/tools-artbio/tree/main/tools/oases | -1.4.0 | -oases | -0.2.09 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | ont_fast5_api | -ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 | -ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. | -- | - | - | - | - | - | - | To update | -https://github.com/nanoporetech/ont_fast5_api/ | -Nanopore | -ont_fast5_api | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api | -3.1.3 | -ont-fast5-api | -4.1.3 | -- | - | 0 | -0 | -4 | -0 | -0 | -0 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -4 | -39 | -2654 | -- |
- | pbtk | -bam2fastx | -Convert PacBio Bam File to fasta or fastq file | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/PacificBiosciences/pbtk | -Convert Formats, Fasta Manipulation, Fastq Manipulation | -bam2fastx | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk | -3.1.1 | -pbtk | -3.1.1 | -- | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | plasmidspades | -plasmidspades | -Genome assembler for assemblying plasmid | -- | - | - | - | - | - | - | To update | -- | Assembly | -plasmidspades | -nml | -- | https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades | -1.1 | -spades | -4.0.0 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | porechop | -porechop | -Porechop - Finding and removing adapters from Oxford Nanopore reads | -- | - | - | - | - | - | - | To update | -https://github.com/rrwick/Porechop | -Fasta Manipulation, Fastq Manipulation | -porechop | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop | -- | porechop | -0.2.4 | -- | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1046 | -185468 | -- |
- | poretools | -poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot | -A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. | -poretools | -poretools | -- | Poretools | -Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. | -Nucleic acid sequence analysis | -DNA, Sequencing | -Up-to-date | -https://poretools.readthedocs.io/en/latest/ | -Fasta Manipulation, Fastq Manipulation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools | -0.6.1a1 | -poretools | -0.6.1a1 | -Nucleic acid sequence analysis | -DNA, Sequencing | -13 | -13 | -13 | -0 | -13 | -13 | -13 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -13 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -13 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -13 | -13 | -409 | -18773 | -- |
- | prinseq | -prinseq | -PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets | -prinseq | -prinseq | -- | PRINSEQ | -PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. | -Read pre-processing, Sequence trimming, Sequence contamination filtering | -Transcriptomics, Metagenomics, Genomics | -To update | -http://prinseq.sourceforge.net/manual.html | -Fastq Manipulation, Metagenomics | -prinseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq | -@TOOL_VERSION+galaxy2 | -prinseq | -0.20.4 | -Read pre-processing, Sequence trimming, Sequence contamination filtering | -Transcriptomics, Metagenomics | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -70 | -7881 | -- |
- | promer | -promer4_substitutions | -Aligns two sets of contigs and reports amino acid substitutions between them | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/promer | -Assembly | -promer | -nml | -https://github.com/phac-nml/promer | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer | -1.2 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | purge_dups | -purge_dups | -Purge haplotigs and overlaps in an assembly based on read depth | -purge_dups | -purge_dups | -- | purge_dups | -Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences | -Genome assembly, Read binning, Scaffolding | -Sequence assembly | -Up-to-date | -https://github.com/dfguan/purge_dups | -Assembly | -purge_dups | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups | -1.2.6 | -purge_dups | -1.2.6 | -Genome assembly, Read binning, Scaffolding | -Sequence assembly | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -167 | -16800 | -- |
- | pycoqc | -pycoqc | -QC metrics for ONT Basecalling | -pycoqc | -pycoqc | -- | pycoQC | -PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. | -Sequencing quality control, Statistical calculation | -Sequence analysis, Data quality management, Sequencing | -Up-to-date | -https://github.com/tleonardi/pycoQC | -Nanopore | -pycoqc | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc | -2.5.2 | -pycoqc | -2.5.2 | -Sequencing quality control, Statistical calculation | -Sequence analysis, Data quality management, Sequencing | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -350 | -21123 | -- |
- | qfilt | -qfilt | -Filter sequencing data | -- | - | - | - | - | - | - | To update | -https://github.com/veg/qfilt | -Fastq Manipulation | -qfilt | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt | -1.0.0+galaxy1 | -qfilt | -0.0.1 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | quast | -quast | -Quast (Quality ASsessment Tool) evaluates genome assemblies. | -quast | -quast | -- | QUAST | -QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. | -Visualisation, Sequence assembly validation | -Sequence assembly | -Up-to-date | -http://quast.bioinf.spbau.ru/ | -Assembly | -quast | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast | -5.2.0 | -quast | -5.2.0 | -Visualisation, Sequence assembly validation | -Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -3567 | -51567 | -- |
- | quickmerge | -quickmerge | -Merge long-read and hybrid assemblies to increase contiguity | -quickmerge | -quickmerge | -- | quickmerge | -Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. | -Genome assembly, Scaffolding, De-novo assembly, Genotyping | -Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype | -Up-to-date | -https://github.com/mahulchak/quickmerge | -Assembly | -quickmerge | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge | -0.3 | -quickmerge | -0.3 | -Genome assembly, Scaffolding, De-novo assembly, Genotyping | -Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -- |
- | ragtag | -ragtag | -Reference-guided scaffolding of draft genomes tool. | -ragtag | -ragtag | -- | ragtag | -RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. | -Genome assembly | -Sequence assembly | -Up-to-date | -https://github.com/malonge/RagTag | -Assembly | -ragtag | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag | -2.1.0 | -ragtag | -2.1.0 | -Genome assembly | -Sequence assembly | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -237 | -2833 | -- |
- | raven | -raven | -Raven is a de novo genome assembler for long uncorrected reads. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/lbcb-sci/raven | -Assembly | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven | -1.8.3 | -raven-assembler | -1.8.3 | -- | - | 0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -262 | -6902 | -- |
- | rcorrector | -rcorrector | -Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. | -rcorrector | -rcorrector | -- | Rcorrector | -This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. | -Sequencing error detection | -RNA, RNA-Seq, Sequencing | -To update | -https://github.com/mourisl/Rcorrector | -Fastq Manipulation | -rcorrector | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector | -1.0.3+galaxy1 | -rcorrector | -1.0.7 | -Sequencing error detection | -RNA, RNA-Seq | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -30 | -569 | -- |
- | rnaquast | -rna_quast | -rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. | -rnaQUAST | -rnaQUAST | -- | rnaQUAST | -Quality assessment tool for de novo transcriptome assemblies. | -De-novo assembly, Transcriptome assembly, Sequence assembly validation | -Sequence assembly, Transcriptomics, RNA-seq | -Up-to-date | -https://github.com/ablab/rnaquast | -Assembly, RNA | -rnaquast | -iuc | -https://git.ufz.de/lehmanju/rnaquast | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast | -2.2.3 | -rnaquast | -2.2.3 | -De-novo assembly, Transcriptome assembly, Sequence assembly validation | -Sequence assembly, Transcriptomics | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -109 | -1110 | -- |
- | salsa2 | -salsa | -A tool to scaffold long read assemblies with Hi-C | -SALSA | -SALSA | -- | SALSA | -> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch | -Genome assembly, De-novo assembly, Scaffolding | -Sequence assembly, DNA binding sites, Mapping | -Up-to-date | -https://github.com/marbl/SALSA | -Assembly | -salsa | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 | -2.3 | -salsa2 | -2.3 | -Genome assembly, De-novo assembly, Scaffolding | -Sequence assembly, DNA binding sites, Mapping | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -84 | -454 | -- |
- | samblaster | -samblaster | -samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files | -samblaster | -samblaster | -- | SAMBLASTER | -A tool to mark duplicates and extract discordant and split reads from SAM files. | -Split read mapping | -DNA, Sequencing, Mapping | -To update | -https://github.com/GregoryFaust/samblaster | -SAM, Fastq Manipulation, Variant Analysis | -samblaster | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster | -0.1.24 | -samblaster | -0.1.26 | -Split read mapping | -DNA, Sequencing, Mapping | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | sample_seqs | -sample_seqs | -Sub-sample sequences files (e.g. to reduce coverage) | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs | -Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis | -sample_seqs | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs | -https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs | -0.2.6 | -biopython | -1.70 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -149 | -3765 | -- |
- | samtools_depad | -samtools_depad | -Re-align a SAM/BAM file with a padded reference (using samtools depad) | -- | - | - | - | - | - | - | To update | -http://www.htslib.org/ | -Assembly, SAM, Sequence Analysis | -samtools_depad | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad | -0.0.5 | -samtools | -1.20 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | samtools_depth | -samtools_depth | -Coverage depth via samtools | -- | - | - | - | - | - | - | To update | -http://www.htslib.org/ | -Assembly, Sequence Analysis, SAM | -samtools_depth | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth | -0.0.3 | -samtools | -1.20 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -296 | -4948 | -- |
- | samtools_idxstats | -samtools_idxstats | -BAM mapping statistics (using samtools idxstats) | -- | - | - | - | - | - | - | To update | -http://www.htslib.org/ | -Assembly, Next Gen Mappers, SAM | -samtools_idxstats | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats | -0.0.6 | -samtools | -1.20 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1450 | -48426 | -- |
- | seq_filter_by_id | -seq_filter_by_id | -Filter sequences by ID | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id | -Fasta Manipulation, Sequence Analysis, Text Manipulation | -seq_filter_by_id | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id | -0.2.9 | -biopython | -1.70 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -306 | -25302 | -- |
- | seq_filter_by_mapping | -seq_filter_by_mapping | -Filter sequencing reads using SAM/BAM mapping files | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping | -Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis | -seq_filter_by_mapping | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping | -0.0.8 | -biopython | -1.70 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -82 | -3784 | -- |
- | seq_length | -seq_length | -Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length | -Fasta Manipulation, Fastq Manipulation, Sequence Analysis | -seq_length | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length | -0.0.5 | -biopython | -1.70 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | seq_primer_clip | -seq_primer_clip | -Trim off 5' or 3' primers | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip | -Assembly, Fasta Manipulation, Text Manipulation | -seq_primer_clip | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip | -0.0.18 | -galaxy_sequence_utils | -1.1.5 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | seq_rename | -seq_rename | -Rename sequences with ID mapping from a tabular file | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename | -Fasta Manipulation, Sequence Analysis, Text Manipulation | -seq_rename | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename | -0.0.10 | -galaxy_sequence_utils | -1.1.5 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -- |
- | seq_select_by_id | -seq_select_by_id | -Select sequences by ID | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id | -Fasta Manipulation, Sequence Analysis, Text Manipulation | -seq_select_by_id | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id | -0.0.15 | -biopython | -1.70 | -- | - | 0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | seqprep | -seqprep | -Tool for merging paired-end Illumina reads and trimming adapters. | -seqprep | -seqprep | -- | SeqPrep | -Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. | -Nucleic acid design | -Genomics, Sequence assembly, Sequencing, Probes and primers | -Up-to-date | -https://github.com/jstjohn/SeqPrep | -Fastq Manipulation, Sequence Analysis | -seqprep | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep | -1.3.2 | -seqprep | -1.3.2 | -Nucleic acid design | -Genomics, Sequence assembly, Sequencing, Probes and primers | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | sequence_format_converter | -sequence_format_converter | -various fasta to tabular conversions | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Convert Formats, Fasta Manipulation | -sequence_format_converter | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter | -https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter | -2.2.0 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | shasta | -shasta | -Fast de novo assembly of long read sequencing data | -- | - | - | - | - | - | - | To update | -https://github.com/chanzuckerberg/shasta | -Assembly, Nanopore | -shasta | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta | -0.6.0 | -shasta | -0.12.0 | -- | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -154 | -763 | -- |
- | short_reads_trim_seq | -trim_reads | -Select high quality segments | -- | - | - | - | - | - | - | To update | -- | Fastq Manipulation | -short_reads_trim_seq | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq | -1.0.0 | -- | - | - | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -21 | -220 | -- |
- | shovill | -shovill | -Faster de novo assembly pipeline based around Spades | -shovill | -shovill | -- | shovill | -Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. | -Genome assembly | -Genomics, Microbiology, Sequence assembly | -Up-to-date | -https://github.com/tseemann/shovill | -Assembly | -shovill | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill | -1.1.0 | -shovill | -1.1.0 | -Genome assembly | -Genomics, Microbiology, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1008 | -41600 | -- |
- | sickle | -sickle | -A windowed adaptive trimming tool for FASTQ files using quality | -sickle | -sickle | -- | sickle | -A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. | -Sequence trimming | -Data quality management | -To update | -https://github.com/najoshi/sickle | -Fastq Manipulation, Sequence Analysis | -sickle | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle | -1.33.2 | -sickle-trim | -1.33 | -Sequence trimming | -Data quality management | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -1 | -269 | -14982 | -- |
- | smudgeplot | -smudgeplot | -Inference of ploidy and heterozygosity structure using whole genome sequencing | -smudgeplots | -smudgeplots | -- | Smudgeplots | -Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 | -Sequence trimming, Genotyping, k-mer counting | -Sequence assembly, Genetic variation, Mathematics | -Up-to-date | -https://github.com/KamilSJaron/smudgeplot | -Assembly | -smudgeplot | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot | -0.2.5 | -smudgeplot | -0.2.5 | -Sequence trimming, Genotyping, k-mer counting | -Sequence assembly, Genetic variation, Mathematics | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -22 | -203 | -- |
- | spades | -spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades | -SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. | -spades | -rnaspades, spades, biosyntheticspades, metaspades, rnaviralspades, plasmidspades, coronaspades, metaviralspades, metaplasmidspades | -- | SPAdes | -St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. | -Genome assembly | -Sequence assembly | -To update | -https://github.com/ablab/spades | -Assembly, RNA, Metagenomics | -spades | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades | -3.15.5 | -spades | -4.0.0 | -Genome assembly | -Sequence assembly | -9 | -9 | -9 | -9 | -9 | -9 | -9 | -9 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -3 | -8 | -0 | -0 | -2 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -9 | -3 | -3547 | -72953 | -- |
- | spades_header_fixer | -spades_header_fixer | -Fixes Spades Fasta ids | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools | -Fasta Manipulation | -spades_fasta_header_fixer | -nml | -https://github.com/phac-nml/galaxy_tools | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer | -1.1.2+galaxy1 | -sed | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | split_paired_reads | -split_paired_reads | -Split paired end reads | -- | - | - | - | - | - | - | To update | -- | Fastq Manipulation | -split_paired_reads | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads | -1.0.0 | -- | - | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | sra-tools | -fasterq_dump, fastq_dump, sam_dump | -NCBI Sequence Read Archive toolkit utilities | -sra-tools | -sra-tools | -- | SRA Software Toolkit | -The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | -Data handling | -DNA, Genomics, Sequencing | -Up-to-date | -https://github.com/ncbi/sra-tools | -Data Source, Fastq Manipulation | -sra_tools | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools | -3.1.1 | -sra-tools | -3.1.1 | -Data handling | -DNA, Genomics, Sequencing | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -3 | -0 | -0 | -3 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -6247 | -350032 | -- |
- | tabular_to_fastq | -tabular_to_fastq | -Tabular to FASTQ converter | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -tabular_to_fastq | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq | -1.1.5 | -galaxy_sequence_utils | -1.1.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -200 | -7388 | -- |
- | tarfast5 | -tarfast5 | -produces a tar.gz archive of fast5 sequence files | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Nanopore | -tarfast5 | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 | -https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 | -0.6.1 | -pigz | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | taxonomy_krona_chart | -taxonomy_krona_chart | -Krona pie chart from taxonomic profile | -krona | -krona | -- | Krona | -Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). | -Visualisation | -Metagenomics | -To update | -http://sourceforge.net/projects/krona/ | -Assembly | -taxonomy_krona_chart | -crs4 | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart | -2.7.1+galaxy0 | -krona | -2.8.1 | -Visualisation | -Metagenomics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -1 | -1801 | -27426 | -- |
- | tgsgapcloser | -tgsgapcloser | -TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. | -TGS-GapCloser | -TGS-GapCloser | -- | TGS-GapCloser | -TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. | -Genome assembly, Read mapping, Scaffolding, Localised reassembly | -Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping | -To update | -https://github.com/BGI-Qingdao/TGS-GapCloser | -Assembly | -tgsgapcloser | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser | -https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser | -1.0.3 | -tgsgapcloser | -1.2.1 | -Genome assembly, Read mapping, Scaffolding, Localised reassembly | -Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -36 | -460 | -- |
- | trim_galore | -trim_galore | -Trim Galore adaptive quality and adapter trimmer | -trim_galore | -trim_galore | -- | Trim Galore | -A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. | -Sequence trimming, Primer removal, Read pre-processing | -Sequence analysis | -To update | -http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ | -Sequence Analysis, Fastq Manipulation | -trim_galore | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore | -https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore | -0.6.7 | -trim-galore | -0.6.10 | -Sequence trimming, Primer removal, Read pre-processing | -Sequence analysis | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -2334 | -238699 | -- |
- | trimmomatic | -trimmomatic | -A flexible read trimming tool for Illumina NGS data | -- | - | - | - | - | - | - | Up-to-date | -http://www.usadellab.org/cms/?page=trimmomatic | -Fastq Manipulation | -trimmomatic | -pjbriggs | -https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic | -0.39 | -trimmomatic | -0.39 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -1 | -1 | -5862 | -305866 | -- |
- | trycycler | -trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample | -Trycycler toolkit wrappers | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/rrwick/Trycycler | -Assembly | -trycycler | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler | -0.5.5 | -trycycler | -0.5.5 | -- | - | 0 | -5 | -5 | -5 | -0 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -147 | -8942 | -- |
- | unicycler | -unicycler | -Unicycler is a hybrid assembly pipeline for bacterial genomes. | -unicycler | -unicycler | -- | Unicycler | -A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. | -Genome assembly, Aggregation | -Microbiology, Genomics, Sequencing, Sequence assembly | -Up-to-date | -https://github.com/rrwick/Unicycler | -Assembly | -unicycler | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler | -0.5.0 | -unicycler | -0.5.0 | -Genome assembly, Aggregation | -Microbiology, Genomics, Sequencing, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1558 | -65732 | -- |
- | validate_fasta_database | -validate_fasta_database | -runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. | -- | - | - | - | - | - | - | To update | -- | Fasta Manipulation, Proteomics | -validate_fasta_database | -galaxyp | -- | https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database | -0.1.5 | -validate-fasta-database | -1.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -25 | -86 | -- |
- | velvet | -velvetg, velveth | -de novo genomic assembler specially designed for short read sequencing technologies | -velvet | -velvet | -- | Velvet | -A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. | -Formatting, De-novo assembly | -Sequence assembly | -To update | -https://www.ebi.ac.uk/~zerbino/velvet/ | -Assembly | -velvet | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet | -- | velvet | -1.2.10 | -Formatting, De-novo assembly | -Sequence assembly | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -2083 | -25420 | -- |
- | velvet_optimiser | -velvetoptimiser | -Automatically optimize Velvet assemblies | -velvetoptimiser | -velvetoptimiser | -- | VelvetOptimiser | -This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. | -Optimisation and refinement, Sequence assembly | -Genomics, Sequence assembly | -To update | -- | Assembly | -velvetoptimiser | -simon-gladman | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser | -2.2.6+galaxy2 | -velvet | -1.2.10 | -Optimisation and refinement, Sequence assembly | -Genomics, Sequence assembly | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -255 | -4741 | -- |
- | verkko | -verkko | -Telomere-to-telomere assembly pipeline | -- | - | - | - | - | - | - | To update | -https://github.com/marbl/verkko | -Assembly | -verkko | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko | -1.3.1 | -verkko | -2.1 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -9 | -22 | -- |
- | wtdbg | -wtdbg | -WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. | -wtdbg2 | -wtdbg2 | -- | wtdbg2 | -Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. | -Genome assembly, De-novo assembly | -Sequence assembly, Sequencing | -Up-to-date | -https://github.com/ruanjue/wtdbg2 | -Assembly | -wtdbg | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg | -https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg | -2.5 | -wtdbg | -2.5 | -Genome assembly, De-novo assembly | -Sequence assembly, Sequencing | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -116 | -1660 | -- |
- | xpore | -xpore_dataprep, xpore_diffmod | -Identification and quantification of differential RNA modifications from direct RNA sequencing | -- | - | - | - | - | - | - | To update | -https://github.com/GoekeLab/xpore | -Nanopore | -xpore | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore | -https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore | -2.1+galaxy0 | -xpore | -2.1 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | yac_clipper | -yac | -Clips 3' adapters for small RNA sequencing reads. | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -RNA, Fastq Manipulation | -yac_clipper | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper | -https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper | -2.5.1 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | yahs | -yahs | -Yet Another Hi-C scaffolding tool | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/c-zhou/yahs | -Assembly | -yahs | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs | -1.2a.2 | -yahs | -1.2a.2 | -- | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -64 | -344 | -- |
Expand | -Galaxy wrapper id | -Galaxy tool ids | -Description | -bio.tool id | -bio.tool ids | -biii | -bio.tool name | -bio.tool description | -EDAM operation | -EDAM topic | -Status | -Source | -ToolShed categories | -ToolShed id | -Galaxy wrapper owner | -Galaxy wrapper source | -Galaxy wrapper parsed folder | -Galaxy wrapper version | -Conda id | -Conda version | -EDAM operation (no superclasses) | -EDAM topic (no superclasses) | -Available on UseGalaxy.org (Main) | -Available on UseGalaxy.org.au | -Available on UseGalaxy.eu | -Available on UseGalaxy.fr | -Tools available on UseGalaxy.org (Main) | -Tools available on UseGalaxy.org.au | -Tools available on UseGalaxy.eu | -Tools available on UseGalaxy.fr | -Tools available on ANASTASIA | -Tools available on APOSTL | -Tools available on ARGs-OAP | -Tools available on BF2I-MAP | -Tools available on BioBix | -Tools available on CIRM-CFBP | -Tools available on Center for Phage Technology (CPT) | -Tools available on ChemFlow | -Tools available on Coloc-stats | -Tools available on CorGAT | -Tools available on CropGalaxy | -Tools available on Dintor | -Tools available on FreeBioinfo | -Tools available on GASLINI | -Tools available on Galaxy@AuBi | -Tools available on Galaxy@Pasteur | -Tools available on GalaxyTrakr | -Tools available on Genomic Hyperbrowser | -Tools available on GigaGalaxy | -Tools available on HyPhy HIV NGS Tools | -Tools available on IPK Galaxy Blast Suite | -Tools available on ImmPort Galaxy | -Tools available on InteractoMIX | -Tools available on MISSISSIPPI | -Tools available on Mandoiu Lab | -Tools available on MiModD NacreousMap | -Tools available on Oqtans | -Tools available on Palfinder | -Tools available on PepSimili | -Tools available on PhagePromotor | -Tools available on Protologger | -Tools available on UseGalaxy.be | -Tools available on UseGalaxy.cz | -Tools available on UseGalaxy.no | -No. of tool users (2022-2023) (usegalaxy.eu) | -Total tool usage (usegalaxy.eu) | -Deprecated | -
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
- | EMLassemblyline | -eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template | -Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa | -- | - | - | - | - | - | - | To update | -https://github.com/EDIorg/EMLassemblyline | -Ecology | -emlassemblyline | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline | -0.1.1+galaxy0 | -r-emlassemblyline | -- | - | - | 0 | -0 | -9 | -9 | -0 | -0 | -9 | -9 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -5 | -102 | -- |
- | Ecoregionalization_workflow | -ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker | -Tools to compute ecoregionalization with BRT model predictions and clustering. | -- | - | - | - | - | - | - | To update | -https://github.com/PaulineSGN/Workflow_Galaxy | -Ecology | -ecoregionalization | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow | -0.1.0+galaxy0 | -r-base | -- | - | - | 0 | -0 | -6 | -5 | -0 | -0 | -6 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -0 | -82 | -- |
- | Geom_mean_workflow | -Map_shp, Mean_geom, bar_plot | -Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). | -- | - | - | - | - | - | - | To update | -https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom | -Ecology | -Geometric means (Dead wood) | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow | -0.1.0+galaxy0 | -r-base | -- | - | - | 0 | -0 | -3 | -3 | -0 | -0 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | PAMPA | -pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm | -Tools to compute and analyse biodiversity metrics | -- | - | - | - | - | - | - | To update | -- | Ecology | -pampa | -ecology | -https://github.com/ColineRoyaux/PAMPA-Galaxy | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA | -0.0.2 | -- | - | - | - | 0 | -5 | -5 | -5 | -0 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -4 | -73 | -1004 | -- |
- | TrimNs | -trimns | -TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline | -- | - | - | - | - | - | - | To update | -https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs | -Assembly | -trimns | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs | -0.1.0 | -trimns_vgp | -1.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -8 | -42 | -- |
- | abacas | -abacas | -Order and Orientate Contigs | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/abacas | -Assembly | -abacas | -nml | -https://github.com/phac-nml/abacas | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas | -1.1 | -mummer | -3.23 | -- | - | 0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | abyss | -abyss-pe | -Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler | -abyss | -abyss | -- | ABySS | -De novo genome sequence assembler using short reads. | -Genome assembly, De-novo assembly, Scaffolding | -Sequence assembly | -Up-to-date | -http://www.bcgsc.ca/platform/bioinfo/software/abyss | -Assembly | -abyss | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss | -2.3.7 | -abyss | -2.3.7 | -Genome assembly, De-novo assembly, Scaffolding | -Sequence assembly | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -391 | -4278 | -- |
- | annotatemyids | -annotatemyids | -annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages | -annotatemyids | -annotatemyids | -- | annotatemyids | -This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. | -Annotation | -- | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids | -Genome annotation | -annotatemyids | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids | -3.18.0 | -bioconductor-org.hs.eg.db | -- | Annotation | -- | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1175 | -25975 | -- |
- | aquainfra_importer | -aquainfra_importer | -A data source tool for downloading datasets via the AquaINFRA Interaction Platform. | -- | - | - | - | - | - | - | To update | -https://github.com/AquaINFRA/galaxy | -Ecology | -- | ecology | -https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer | -1.0 | -- | - | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | assembly-stats | -assembly_stats | -Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. | -- | - | - | - | - | - | - | To update | -https://github.com/rjchallis/assembly-stats | -Assembly | -assembly_stats | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats | -17.02 | -rjchallis-assembly-stats | -- | - | - | 0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | assemblystats | -assemblystats | -Summarise an assembly (e.g. N50 metrics) | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools | -Assembly | -assemblystats | -nml | -https://github.com/phac-nml/galaxy_tools | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats | -1.1.0 | -perl-bioperl | -1.7.8 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | bam2mappingstats | -bam2mappingstats | -Generates mapping stats from a bam file. | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools | -Assembly | -bam2mappingstats | -nml | -https://github.com/phac-nml/galaxy_tools | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats | -1.1.0 | -perl | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | baseline_calculator | -tt_baseline | -Toxicity prediction using QSAR models | -- | - | - | - | - | - | - | To update | -https://github.com/bernt-matthias/mb-galaxy-tools | -Ecology, Text Manipulation | -baseline_toxicity_calculator | -mbernt | -https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator | -https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator | -0.1.0+galaxy0 | -pandas | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | bionano | -bionano_scaffold | -Bionano Solve is a set of tools for analyzing Bionano data | -- | - | - | - | - | - | - | To update | -https://bionanogenomics.com/ | -Assembly | -bionano | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/bionano | -https://github.com/bgruening/galaxytools/tree/master/tools/bionano | -3.7.0 | -- | - | - | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -112 | -531 | -- |
- | biotradis | -bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites | -Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. | -biotradis | -biotradis | -- | biotradis | -The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. | -Sequence analysis | -Mobile genetic elements, Workflows | -Up-to-date | -https://www.sanger.ac.uk/science/tools/bio-tradis | -Genome annotation | -biotradis | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis | -1.4.5 | -biotradis | -1.4.5 | -Sequence analysis | -Mobile genetic elements, Workflows | -3 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | biscot | -biscot | -Bionano scaffolding correction tool | -- | - | - | - | - | - | - | To update | -https://github.com/institut-de-genomique/biscot | -Assembly | -biscot | -iuc | -https://github.com/bgruening/iuc/tree/master/tools/biscot | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot | -2.3.3 | -biscot | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -3 | -- |
- | blast_to_scaffold | -blast2scaffold | -Generate DNA scaffold from blastn or tblastx alignments of Contigs | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -RNA, Sequence Analysis, Assembly | -blast_to_scaffold | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold | -1.1.0 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | blastparser_and_hits | -BlastParser_and_hits | -Parse blast outputs and compile hits | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Assembly, RNA | -blastparser_and_hits | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits | -2.7.1 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | blastx_to_scaffold | -blastx2scaffold | -Generate DNA scaffold from blastx alignment of Contigs | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -RNA, Sequence Analysis, Assembly | -blastx_to_scaffold | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold | -1.1.1 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | blobtoolkit | -blobtoolkit | -Identification and isolation non-target data in draft and publicly available genome assemblies. | -- | - | - | - | - | - | - | To update | -https://blobtoolkit.genomehubs.org/ | -Sequence Analysis, Assembly | -blobtoolkit | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit | -https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit | -4.0.7 | -- | - | - | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -21 | -685 | -- |
- | braker | -braker | -BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . | -- | - | - | - | - | - | - | To update | -https://github.com/Gaius-Augustus/BRAKER | -Genome annotation | -braker | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/braker | -https://github.com/genouest/galaxy-tools/tree/master/tools/braker | -2.1.6 | -- | - | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -17 | -109 | -- |
- | braker3 | -braker3 | -BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . | -braker3 | -braker3 | -- | BRAKER3 | -BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes | -Genome annotation, Gene prediction | -RNA-Seq, Genomics, Structure prediction, Sequence analysis | -To update | -https://github.com/Gaius-Augustus/BRAKER | -Genome annotation | -braker3 | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/braker | -https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 | -3.0.8 | -- | - | Genome annotation, Gene prediction | -RNA-Seq, Genomics, Structure prediction, Sequence analysis | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -10 | -567 | -- |
- | cap3 | -cap3 | -cap3 wrapper | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Assembly | -cap3 | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 | -https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 | -2.0.1 | -cap3 | -10.2011 | -- | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -101 | -7766 | -- |
- | champ_blocs | -cb_dissim, cb_ivr, cb_div | -Compute indicators for turnover boulders fields | -- | - | - | - | - | - | - | To update | -- | Ecology | -- | ecology | -https://github.com/Marie59/champ_blocs | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs | -0.0.0 | -r-base | -- | - | - | 0 | -0 | -3 | -3 | -0 | -0 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -19 | -174 | -- |
- | chipseeker | -chipseeker | -A tool for ChIP peak annotation and visualization | -- | - | - | - | - | - | - | To update | -https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html | -ChIP-seq, Genome annotation | -chipseeker | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker | -https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker | -1.32.0 | -bioconductor-chipseeker | -1.38.0 | -- | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -418 | -15690 | -- |
- | circexplorer2 | -circexplorer2 | -Comprehensive and integrative circular RNA analysis toolset. | -circexplorer2 | -circexplorer2 | -- | CIRCexplorer2 | -Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. | -- | RNA splicing, Gene transcripts, Literature and language | -Up-to-date | -https://github.com/YangLab/CIRCexplorer2 | -RNA, Assembly | -circexplorer2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 | -2.3.8 | -circexplorer2 | -2.3.8 | -- | RNA splicing, Gene transcripts, Literature and language | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -16 | -269 | -- |
- | clc_assembly_cell | -clc_assembler, clc_mapper | -Galaxy wrapper for the CLC Assembly Cell suite from CLCBio | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell | -Assembly, Next Gen Mappers, SAM | -clc_assembly_cell | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell | -https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell | -0.0.7 | -samtools | -1.20 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | combine_assembly_stats | -combine_stats | -Combine multiple Assemblystats datasets into a single tabular report | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools | -Assembly | -combine_assemblystats | -nml | -https://github.com/phac-nml/galaxy_tools | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats | -1.0 | -perl-getopt-long | -2.58 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | count_roi_variants | -count_roi_variants | -Count sequence variants in region of interest in BAM file | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants | -Assembly, SAM | -count_roi_variants | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants | -https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants | -0.0.6 | -samtools | -1.20 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | coverage_stats | -coverage_stats | -BAM coverage statistics using samtools idxstats and depth | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats | -Assembly, SAM | -coverage_stats | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats | -https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats | -0.1.0 | -samtools | -1.20 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | data_exploration | -tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs | -Explore data through multiple statistical tools | -- | - | - | - | - | - | - | To update | -- | Ecology | -- | ecology | -https://github.com/Marie59/Data_explo_tools | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration | -0.0.0 | -r-tangles | -- | - | - | 0 | -0 | -6 | -6 | -0 | -0 | -6 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -0 | -146 | -658 | -- |
- | deepsig | -deepsig | -Predictor of signal peptides in proteins based on deep learning | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/BolognaBiocomp/deepsig | -Genome annotation | -deepsig | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig | -1.2.5 | -deepsig | -1.2.5 | -- | - | 0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -- |
- | disco | -disco | -DISCO is a overlap-layout-consensus (OLC) metagenome assembler | -disco | -disco | -- | DISCO | -DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. | -Protein sequence analysis | -Structure determination | -To update | -http://disco.omicsbio.org/ | -Metagenomics, Assembly | -disco | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco | -- | disco | -1.2 | -Protein sequence analysis | -Structure determination | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -42 | -369 | -- |
- | dose_responses | -dr_curve | -A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/bernt-matthias/mb-galaxy-tools | -Ecology | -dose_response_analysis_tool | -ufz | -https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator | -https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses | -3.0_1 | -r-drc | -3.0_1 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | ear | -make_ear | -A tool to compile assembly reports and stastics from assembly pipeline | -- | - | - | - | - | - | - | To update | -https://github.com/ERGA-consortium/EARs/tree/main | -Sequence Analysis, Assembly | -erga_ear | -iuc | -https://github.com/ERGA-consortium/EARs/tree/main | -https://github.com/bgruening/galaxytools/tree/master/tools/ear | -1.0.0 | -reportlab | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | fastk | -fastk_fastk | -FastK: A K-mer counter (for HQ assembly data sets) | -- | - | - | - | - | - | - | To update | -https://github.com/thegenemyers/FASTK | -Assembly | -fastk | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk | -1.0.0 | -fastk | -1.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | fermikit | -fermi2, fermikit_variants | -FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/lh3/fermikit | -Assembly, Variant Analysis | -fermikit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit | -r193 | -fermi2 | -r193 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | filter_spades_repeats | -filter_spades_repeat | -Remove short and repeat contigs/scaffolds | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools/ | -Assembly | -filter_spades_repeats | -nml | -https://github.com/phac-nml/galaxy_tools/ | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats | -1.0.1 | -perl-bioperl | -1.7.8 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | flash | -flash | -Fast Length Adjustment of SHort reads | -flash | -flash | -- | FLASH | -Identifies paired-end reads which overlap in the middle, converting them to single long reads | -Read pre-processing, Sequence merging, Sequence assembly | -Sequencing, Sequence assembly | -Up-to-date | -https://ccb.jhu.edu/software/FLASH/ | -Assembly, Fastq Manipulation | -flash | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash | -1.2.11 | -flash | -1.2.11 | -Read pre-processing, Sequence merging, Sequence assembly | -Sequencing, Sequence assembly | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -74 | -13759 | -- |
- | flye | -flye | -Assembly of long and error-prone reads. | -Flye | -Flye | -- | Flye | -Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. | -Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly | -Sequence assembly, Metagenomics, Whole genome sequencing, Genomics | -To update | -https://github.com/fenderglass/Flye/ | -Assembly | -flye | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/flye | -https://github.com/bgruening/galaxytools/tree/master/tools/flye | -2.9.3 | -flye | -2.9.4 | -Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly | -Sequence assembly, Metagenomics, Whole genome sequencing | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1499 | -20904 | -- |
- | funannotate | -funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort | -Funannotate is a genome prediction, annotation, and comparison software package. | -funannotate | -funannotate | -- | funannotate | -funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). | -Genome annotation | -Genomics | -To update | -https://funannotate.readthedocs.io | -Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate | -1.8.15 | -- | - | Genome annotation | -Genomics | -3 | -5 | -5 | -5 | -3 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -900 | -5906 | -- |
- | gdal | -gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo | -Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. | -- | - | - | - | - | - | - | To update | -https://www.gdal.org | -Ecology | -gdal | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal | -3.0.0 | -- | - | - | - | 0 | -0 | -8 | -8 | -0 | -0 | -8 | -8 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -8 | -8 | -10 | -1475 | -- |
- | getorganelle | -get_annotated_regions_from_gb, get_organelle_from_reads | -GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. | -getorganelle | -getorganelle | -- | GetOrganelle | -A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. | -De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming | -Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms | -Up-to-date | -https://github.com/Kinggerm/GetOrganelle | -Assembly | -getorganelle | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle | -1.7.7.1 | -getorganelle | -1.7.7.1 | -De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming | -Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms | -0 | -2 | -2 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -18 | -495 | -- |
- | goenrichment | -goenrichment, goslimmer | -Performs GO Enrichment analysis. | -goenrichment | -goenrichment | -- | GOEnrichment | -GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de CiĂŞncia. | -Gene-set enrichment analysis | -Transcriptomics | -Up-to-date | -https://github.com/DanFaria/GOEnrichment | -Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment | -2.0.1 | -goenrichment | -2.0.1 | -Gene-set enrichment analysis | -Transcriptomics | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -408 | -5484 | -- |
- | graphmap | -graphmap_align, graphmap_overlap | -Mapper for long, error-prone reads. | -graphmap | -graphmap | -- | graphmap | -Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 | -Sequence trimming, EST assembly, Read mapping | -Gene transcripts, RNA-Seq, RNA splicing | -To update | -https://github.com/isovic/graphmap/ | -Assembly | -graphmap | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/graphmap | -https://github.com/bgruening/galaxytools/tree/master/tools/graphmap | -0.5.2 | -graphmap | -0.6.3 | -Sequence trimming, EST assembly, Read mapping | -Gene transcripts, RNA-Seq, RNA splicing | -0 | -0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -136 | -6651 | -- |
- | hapcut2 | -hapcut2 | -Robust and accurate haplotype assembly for diverse sequencing technologies | -hapcut2 | -hapcut2 | -- | HapCUT2 | -HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md | -Haplotype mapping, Variant classification | -- | Up-to-date | -https://github.com/vibansal/HapCUT2 | -Assembly | -hapcut2 | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 | -1.3.4 | -hapcut2 | -1.3.4 | -Haplotype mapping, Variant classification | -- | 0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | hapog | -hapog | -Hapo-G - Haplotype-Aware Polishing of Genomes | -hapog | -hapog | -- | Hapo-G | -Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. | -Genome assembly, Optimisation and refinement | -Sequence assembly, Genomics | -Up-to-date | -https://github.com/institut-de-genomique/HAPO-G | -Assembly | -hapog | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog | -1.3.8 | -hapog | -1.3.8 | -Genome assembly, Optimisation and refinement | -Sequence assembly, Genomics | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -36 | -295 | -- |
- | helixer | -helixer | -Gene calling with Deep Neural Networks | -helixer | -helixer | -- | Helixer | -Deep Learning to predict gene annotations | -Gene prediction, Genome annotation | -Sequence analysis, Gene transcripts | -To update | -https://github.com/weberlab-hhu/Helixer | -Genome annotation | -helixer | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/helixer | -https://github.com/genouest/galaxy-tools/tree/master/tools/helixer | -0.3.3 | -- | - | Gene prediction, Genome annotation | -Sequence analysis, Gene transcripts | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -93 | -- |
- | hifiasm | -hifiasm | -A fast haplotype-resolved de novo assembler | -- | - | - | - | - | - | - | To update | -https://github.com/chhylp123/hifiasm | -Assembly | -hifiasm | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm | -https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm | -0.19.8 | -hifiasm | -0.19.9 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -297 | -1410 | -- |
- | hirondelle_crim_ogc_api_processes | -hirondelle_crim | -This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. | -- | - | - | - | - | - | - | To update | -https://github.com/AquaINFRA/galaxy | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes | -0.1.0 | -r-base | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | hisat | -hisat | -HISAT is a fast and sensitive spliced alignment program. | -- | - | - | - | - | - | - | To update | -http://ccb.jhu.edu/software/hisat/index.shtml | -Assembly | -hisat | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat | -1.0.3 | -hisat | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -228 | -- |
- | hisat2 | -hisat2 | -HISAT2 is a fast and sensitive spliced alignment program. | -hisat2 | -hisat2 | -- | HISAT2 | -Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). | -Sequence alignment | -RNA-seq | -Up-to-date | -http://ccb.jhu.edu/software/hisat2/ | -Assembly | -hisat2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 | -2.2.1 | -hisat2 | -2.2.1 | -Sequence alignment | -- | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -4183 | -299104 | -- |
- | hypo | -hypo | -Super Fast & Accurate Polisher for Long Read Genome Assemblies | -HyPo | -HyPo | -- | HyPo | -HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. | -Optimisation and refinement, Genome assembly | -Sequence assembly, Genomics | -Up-to-date | -https://github.com/kensung-lab/hypo | -Assembly | -hypo | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo | -1.0.3 | -hypo | -1.0.3 | -Optimisation and refinement, Genome assembly | -Sequence assembly, Genomics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -39 | -354 | -- |
- | icescreen | -icescreen | -ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. | -icescreen | -icescreen | -- | ICEscreen | -A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. | -Database search, Protein feature detection | -Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation | -To update | -https://icescreen.migale.inrae.fr/ | -Genome annotation | -icescreen | -iuc | -https://forgemia.inra.fr/ices_imes_analysis/icescreen | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen | -1.3.1 | -icescreen | -1.3.2 | -Database search, Protein feature detection | -Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | idba_ud | -idba_hybrid, idba_tran, idba_ud | -Wrappers for the idba assembler variants. | -idba | -idba | -- | IDBA | -A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. | -Sequence assembly | -Sequence assembly | -To update | -https://i.cs.hku.hk/~alse/hkubrg/projects/index.html | -Assembly | -idba | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud | -- | idba | -1.1.3 | -Sequence assembly | -Sequence assembly | -3 | -0 | -3 | -3 | -3 | -0 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -69 | -1127 | -- |
- | instagraal | -instagraal | -Large genome reassembly based on Hi-C data | -instagraal | -instagraal | -- | instaGRAAL | -Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) | -Genome assembly, Mapping assembly, Genetic mapping, Scaffolding | -Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites | -To update | -https://github.com/koszullab/instaGRAAL | -Assembly | -instagraal | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/instagraal | -https://github.com/bgruening/galaxytools/tree/master/tools/instagraal | -0.1.6 | -- | - | Genome assembly, Mapping assembly, Genetic mapping, Scaffolding | -Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -14 | -139 | -- |
- | interpolation | -interpolation_run_idw_interpolation | -Run IDW interpolation based on a .csv and .geojson file | -- | - | - | - | - | - | - | To update | -https://github.com/AquaINFRA/galaxy | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation | -1.0 | -r-getopt | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | jellyfish | -jellyfish | -Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA | -Jellyfish | -Jellyfish | -- | Jellyfish | -A command-line algorithm for counting k-mers in DNA sequence. | -k-mer counting | -Sequence analysis, Genomics | -To update | -https://github.com/gmarcais/Jellyfish | -Assembly | -jellyfish | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish | -- | kmer-jellyfish | -2.3.1 | -k-mer counting | -Sequence analysis, Genomics | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -91 | -1138 | -- |
- | khmer | -khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median | -In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more | -khmer | -khmer | -- | khmer | -khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. | -Standardisation and normalisation, De-novo assembly | -Sequence assembly | -Up-to-date | -https://khmer.readthedocs.org/ | -Assembly, Next Gen Mappers | -khmer | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer | -3.0.0a3 | -khmer | -3.0.0a3 | -Standardisation and normalisation, De-novo assembly | -Sequence assembly | -8 | -8 | -8 | -0 | -8 | -8 | -8 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -8 | -8 | -63 | -2022 | -- |
- | links | -links | -Scaffold genome assemblies with long reads. | -links | -links | -- | LINKS | -LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. | -Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming | -Sequence assembly, Mapping, Sequencing | -Up-to-date | -https://github.com/bcgsc/LINKS | -Assembly | -links | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/links | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/links | -2.0.1 | -links | -2.0.1 | -Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming | -Sequence assembly, Mapping, Sequencing | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -77 | -405 | -- |
- | medenv | -iabiodiv_smartbiodiv_med_environ | -Retrieve environmental data from etopo, cmems and woa | -- | - | - | - | - | - | - | To update | -https://github.com/jeremyfix/medenv | -Ecology, Data Source | -- | ecology | -https://github.com/jeremyfix/medenv | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv | -0.1.0 | -pandas | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | megahit | -megahit | -An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. | -megahit | -megahit | -- | MEGAHIT | -Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. | -Genome assembly | -Metagenomics, Sequencing, Ecology, Sequence assembly | -Up-to-date | -https://github.com/voutcn/megahit | -Sequence Analysis, Assembly, Metagenomics | -megahit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit | -1.2.9 | -megahit | -1.2.9 | -Genome assembly | -Metagenomics, Sequencing, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -1 | -548 | -9530 | -- |
- | megahit_contig2fastg | -megahit_contig2fastg | -A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) | -megahit | -megahit | -- | MEGAHIT | -Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. | -Genome assembly | -Metagenomics, Sequencing, Ecology, Sequence assembly | -To update | -https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp | -Sequence Analysis, Assembly, Metagenomics | -megahit_contig2fastg | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg | -1.1.3 | -megahit | -1.2.9 | -Genome assembly | -Metagenomics, Sequencing, Sequence assembly | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -54 | -475 | -- |
- | merqury | -merqury, merquryplot | -Merqury is a tool for evaluating genomes assemblies based of k-mer operations. | -merqury | -merqury | -- | Merqury | -Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. | -Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly | -Sequence assembly, Whole genome sequencing, Plant biology | -Up-to-date | -https://github.com/marbl/merqury | -Assembly | -merqury | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury | -1.3 | -merqury | -1.3 | -Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly | -Sequence assembly, Whole genome sequencing, Plant biology | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -244 | -2483 | -- |
- | meryl | -meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode | -Meryl a k-mer counter. | -meryl | -meryl | -- | Meryl | -Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. | -k-mer counting | -Whole genome sequencing, Genomics, Sequence analysis, Sequencing | -Up-to-date | -https://github.com/marbl/meryl | -Assembly | -meryl | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl | -1.3 | -merqury | -1.3 | -k-mer counting | -Whole genome sequencing, Genomics, Sequence analysis | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | metaeuk | -metaeuk_easy_predict | -MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. | -MetaEuk | -MetaEuk | -- | MetaEuk | -MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics | -Homology-based gene prediction | -Metagenomics, Gene and protein families | -To update | -https://github.com/soedinglab/metaeuk | -Sequence Analysis, Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk | -5.34c21f2 | -metaeuk | -6.a5d39d9 | -Homology-based gene prediction | -Metagenomics, Gene and protein families | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -16 | -184 | -- |
- | minia | -minia | -Short-read assembler based on a de Bruijn graph | -minia | -minia | -- | Minia | -Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | -Genome assembly | -Sequence assembly | -Up-to-date | -https://gatb.inria.fr/software/minia/ | -Assembly | -minia | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia | -3.2.6 | -minia | -3.2.6 | -Genome assembly | -Sequence assembly | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -109 | -2206 | -- |
- | miniasm | -miniasm | -Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) | -miniasm | -miniasm | -- | miniasm | -Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. | -De-novo assembly | -Genomics, Sequence assembly | -To update | -https://github.com/lh3/miniasm | -Assembly | -miniasm | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm | -0.3_r179 | -miniasm | -0.3 | -De-novo assembly | -Genomics, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -178 | -11938 | -- |
- | mitobim | -mitobim | -assemble mitochondrial genomes | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/chrishah/MITObim | -Assembly | -mitobim | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim | -1.9.1 | -mitobim | -1.9.1 | -- | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -66 | -881 | -- |
- | mitohifi | -mitohifi | -Assembly mitogenomes from Pacbio HiFi read. | -- | - | - | - | - | - | - | To update | -https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 | -Assembly | -mitohifi | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi | -https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi | -3 | -- | - | - | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -56 | -613 | -- |
- | necat | -necat | -Error correction and de-novo assembly for ONT Nanopore reads | -necat | -necat | -- | NECAT | -NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. | -De-novo assembly | -Sequence assembly | -Up-to-date | -https://github.com/xiaochuanle/NECAT | -Assembly | -necat | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat | -0.0.1_update20200803 | -necat | -0.0.1_update20200803 | -De-novo assembly | -Sequence assembly | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -95 | -667 | -- |
- | nextdenovo | -nextdenovo | -String graph-based de novo assembler for long reads | -nextdenovo | -nextdenovo | -- | NextDenovo | -NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. | -De-novo assembly, Genome assembly | -Sequencing, Sequence assembly | -To update | -https://github.com/Nextomics/NextDenovo | -Assembly | -nextdenovo | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo | -https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo | -2.5.0 | -nextdenovo | -2.5.2 | -De-novo assembly, Genome assembly | -Sequencing, Sequence assembly | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -84 | -268 | -- |
- | novoplasty | -novoplasty | -NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. | -- | - | - | - | - | - | - | To update | -https://github.com/ndierckx/NOVOPlasty | -Assembly | -novoplasty | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty | -4.3.1 | -novoplasty | -4.3.5 | -- | - | 0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -162 | -6384 | -- |
- | oases | -oasesoptimiserv | -Short read assembler | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Assembly, RNA | -oases | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/oases | -https://github.com/ARTbio/tools-artbio/tree/main/tools/oases | -1.4.0 | -oases | -0.2.09 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | obisindicators | -obisindicators, obis_data | -Compute biodiveristy indicators for marine data from obis | -- | - | - | - | - | - | - | To update | -https://github.com/Marie59/obisindicators | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators | -0.0.2 | -r-base | -- | - | - | 1 | -0 | -2 | -1 | -1 | -0 | -2 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -4 | -45 | -- |
- | ocean | -argo_getdata | -Access, process, visualise oceanographic data for the Earth System | -- | - | - | - | - | - | - | To update | -https://github.com/Marie59/FE-ft-ESG/tree/main/argo | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean | -0.1.15 | -- | - | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -- |
- | ogcProcess_otb_bandmath | -otb_band_math | -Outputs a monoband image which is the result of a mathematical operation on several multi-band images. | -- | - | - | - | - | - | - | To update | -https://github.com/AquaINFRA/galaxy | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath | -1.0 | -r-base | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | ogcProcess_otb_meanShiftSmoothing | -otb_mean_shift_smoothing | -This application smooths an image using the MeanShift algorithm. | -- | - | - | - | - | - | - | To update | -https://github.com/AquaINFRA/galaxy | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing | -1.0 | -r-base | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | pharokka | -pharokka | -rapid standardised annotation tool for bacteriophage genomes and metagenomes | -pharokka | -pharokka | -- | Pharokka | -Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. | -Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly | -Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA | -To update | -https://github.com/gbouras13/pharokka | -Genome annotation | -pharokka | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka | -1.3.2 | -\n pharokka\n | -- | Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly | -Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -74 | -2565 | -- |
- | plasmidspades | -plasmidspades | -Genome assembler for assemblying plasmid | -- | - | - | - | - | - | - | To update | -- | Assembly | -plasmidspades | -nml | -- | https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades | -1.1 | -spades | -4.0.0 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | prodigal | -prodigal | -A protein-coding gene prediction software tool for bacterial and archaeal genomes | -prodigal | -prodigal | -- | Prodigal | -Fast, reliable protein-coding gene prediction for prokaryotic genomes. | -Genome annotation | -Genomics, Sequence analysis | -Up-to-date | -https://github.com/hyattpd/Prodigal | -Genome annotation | -prodigal | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal | -2.6.3 | -prodigal | -2.6.3 | -Genome annotation | -Genomics, Sequence analysis | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | promer | -promer4_substitutions | -Aligns two sets of contigs and reports amino acid substitutions between them | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/promer | -Assembly | -promer | -nml | -https://github.com/phac-nml/promer | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer | -1.2 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | purge_dups | -purge_dups | -Purge haplotigs and overlaps in an assembly based on read depth | -purge_dups | -purge_dups | -- | purge_dups | -Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences | -Genome assembly, Read binning, Scaffolding | -Sequence assembly | -Up-to-date | -https://github.com/dfguan/purge_dups | -Assembly | -purge_dups | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups | -1.2.6 | -purge_dups | -1.2.6 | -Genome assembly, Read binning, Scaffolding | -Sequence assembly | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -167 | -16800 | -- |
- | quast | -quast | -Quast (Quality ASsessment Tool) evaluates genome assemblies. | -quast | -quast | -- | QUAST | -QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. | -Visualisation, Sequence assembly validation | -Sequence assembly | -Up-to-date | -http://quast.bioinf.spbau.ru/ | -Assembly | -quast | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast | -5.2.0 | -quast | -5.2.0 | -Visualisation, Sequence assembly validation | -Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -3567 | -51567 | -- |
- | quickmerge | -quickmerge | -Merge long-read and hybrid assemblies to increase contiguity | -quickmerge | -quickmerge | -- | quickmerge | -Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. | -Genome assembly, Scaffolding, De-novo assembly, Genotyping | -Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype | -Up-to-date | -https://github.com/mahulchak/quickmerge | -Assembly | -quickmerge | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge | -0.3 | -quickmerge | -0.3 | -Genome assembly, Scaffolding, De-novo assembly, Genotyping | -Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -- |
- | ragtag | -ragtag | -Reference-guided scaffolding of draft genomes tool. | -ragtag | -ragtag | -- | ragtag | -RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. | -Genome assembly | -Sequence assembly | -Up-to-date | -https://github.com/malonge/RagTag | -Assembly | -ragtag | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag | -2.1.0 | -ragtag | -2.1.0 | -Genome assembly | -Sequence assembly | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -237 | -2833 | -- |
- | raven | -raven | -Raven is a de novo genome assembler for long uncorrected reads. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/lbcb-sci/raven | -Assembly | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven | -1.8.3 | -raven-assembler | -1.8.3 | -- | - | 0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -262 | -6902 | -- |
- | regionalgam | -regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend | -- | - | - | - | - | - | - | - | To update | -https://github.com/RetoSchmucki/regionalGAM | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam | -1.5 | -r-mgcv | -- | - | - | 0 | -0 | -7 | -7 | -0 | -0 | -7 | -7 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -7 | -7 | -22 | -526 | -- |
- | repeatexplorer2 | -repeatexplorer_clustering | -Tool for annotation of repeats from unassembled shotgun reads. | -- | - | - | - | - | - | - | To update | -https://github.com/repeatexplorer/repex_tarean | -Genome annotation | -repeatexplorer2 | -gga | -https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 | -https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 | -2.3.8 | -- | - | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -16 | -- |
- | repeatmodeler | -repeatmodeler | -RepeatModeler - Model repetitive DNA | -repeatmodeler | -repeatmodeler | -- | RepeatModeler | -De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. | -Repeat sequence detection | -Sequence composition, complexity and repeats, Sequence composition, complexity and repeats | -To update | -https://www.repeatmasker.org/RepeatModeler/ | -Genome annotation | -repeatmodeler | -csbl | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler | -2.0.5 | -- | - | Repeat sequence detection | -Sequence composition, complexity and repeats, Sequence composition, complexity and repeats | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -217 | -1177 | -- |
- | retrieve_bold | -retrieve_bold | -Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers | -- | - | - | - | - | - | - | To update | -https://anaconda.org/conda-forge/r-bold | -Ecology | -retrieve_bold | -ecology | -https://github.com/wpearman1996/MARES_database_pipeline/tree/master | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold | -1.3.0 | -r-base | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | rnaquast | -rna_quast | -rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. | -rnaQUAST | -rnaQUAST | -- | rnaQUAST | -Quality assessment tool for de novo transcriptome assemblies. | -De-novo assembly, Transcriptome assembly, Sequence assembly validation | -Sequence assembly, Transcriptomics, RNA-seq | -Up-to-date | -https://github.com/ablab/rnaquast | -Assembly, RNA | -rnaquast | -iuc | -https://git.ufz.de/lehmanju/rnaquast | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast | -2.2.3 | -rnaquast | -2.2.3 | -De-novo assembly, Transcriptome assembly, Sequence assembly validation | -Sequence assembly, Transcriptomics | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -109 | -1110 | -- |
- | salsa2 | -salsa | -A tool to scaffold long read assemblies with Hi-C | -SALSA | -SALSA | -- | SALSA | -> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch | -Genome assembly, De-novo assembly, Scaffolding | -Sequence assembly, DNA binding sites, Mapping | -Up-to-date | -https://github.com/marbl/SALSA | -Assembly | -salsa | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 | -2.3 | -salsa2 | -2.3 | -Genome assembly, De-novo assembly, Scaffolding | -Sequence assembly, DNA binding sites, Mapping | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -84 | -454 | -- |
- | sample_seqs | -sample_seqs | -Sub-sample sequences files (e.g. to reduce coverage) | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs | -Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis | -sample_seqs | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs | -https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs | -0.2.6 | -biopython | -1.70 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -149 | -3765 | -- |
- | samtools_depad | -samtools_depad | -Re-align a SAM/BAM file with a padded reference (using samtools depad) | -- | - | - | - | - | - | - | To update | -http://www.htslib.org/ | -Assembly, SAM, Sequence Analysis | -samtools_depad | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad | -0.0.5 | -samtools | -1.20 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | samtools_depth | -samtools_depth | -Coverage depth via samtools | -- | - | - | - | - | - | - | To update | -http://www.htslib.org/ | -Assembly, Sequence Analysis, SAM | -samtools_depth | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth | -0.0.3 | -samtools | -1.20 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -296 | -4948 | -- |
- | samtools_idxstats | -samtools_idxstats | -BAM mapping statistics (using samtools idxstats) | -- | - | - | - | - | - | - | To update | -http://www.htslib.org/ | -Assembly, Next Gen Mappers, SAM | -samtools_idxstats | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats | -0.0.6 | -samtools | -1.20 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1450 | -48426 | -- |
- | sdmpredictors | -sdmpredictors_list_layers | -Terrestrial and marine predictors for species distribution modelling. | -- | - | - | - | - | - | - | To update | -https://cran.r-project.org/web/packages/sdmpredictors/index.html | -Ecology | -sdmpredictors | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors | -0.2.15 | -r-base | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | seq_filter_by_mapping | -seq_filter_by_mapping | -Filter sequencing reads using SAM/BAM mapping files | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping | -Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis | -seq_filter_by_mapping | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping | -0.0.8 | -biopython | -1.70 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -82 | -3784 | -- |
- | seq_primer_clip | -seq_primer_clip | -Trim off 5' or 3' primers | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip | -Assembly, Fasta Manipulation, Text Manipulation | -seq_primer_clip | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip | -0.0.18 | -galaxy_sequence_utils | -1.1.5 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | shasta | -shasta | -Fast de novo assembly of long read sequencing data | -- | - | - | - | - | - | - | To update | -https://github.com/chanzuckerberg/shasta | -Assembly, Nanopore | -shasta | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta | -0.6.0 | -shasta | -0.12.0 | -- | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -154 | -763 | -- |
- | shovill | -shovill | -Faster de novo assembly pipeline based around Spades | -shovill | -shovill | -- | shovill | -Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. | -Genome assembly | -Genomics, Microbiology, Sequence assembly | -Up-to-date | -https://github.com/tseemann/shovill | -Assembly | -shovill | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill | -1.1.0 | -shovill | -1.1.0 | -Genome assembly | -Genomics, Microbiology, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1008 | -41600 | -- |
- | smudgeplot | -smudgeplot | -Inference of ploidy and heterozygosity structure using whole genome sequencing | -smudgeplots | -smudgeplots | -- | Smudgeplots | -Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 | -Sequence trimming, Genotyping, k-mer counting | -Sequence assembly, Genetic variation, Mathematics | -Up-to-date | -https://github.com/KamilSJaron/smudgeplot | -Assembly | -smudgeplot | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot | -0.2.5 | -smudgeplot | -0.2.5 | -Sequence trimming, Genotyping, k-mer counting | -Sequence assembly, Genetic variation, Mathematics | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -22 | -203 | -- |
- | spades | -spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades | -SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. | -spades | -rnaspades, spades, biosyntheticspades, metaspades, rnaviralspades, plasmidspades, coronaspades, metaviralspades, metaplasmidspades | -- | SPAdes | -St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. | -Genome assembly | -Sequence assembly | -To update | -https://github.com/ablab/spades | -Assembly, RNA, Metagenomics | -spades | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades | -3.15.5 | -spades | -4.0.0 | -Genome assembly | -Sequence assembly | -9 | -9 | -9 | -9 | -9 | -9 | -9 | -9 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -3 | -8 | -0 | -0 | -2 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -9 | -3 | -3547 | -72953 | -- |
- | spaln | -list_spaln_tables, spaln | -Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. | -- | - | - | - | - | - | - | To update | -http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ | -Sequence Analysis, Genome annotation | -spaln | -iuc | -https://github.com/ogotoh/spaln | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln | -2.4.9 | -python | -- | - | - | 2 | -0 | -2 | -0 | -2 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -34 | -446 | -- |
- | spocc | -spocc_occ | -Get species occurences data | -- | - | - | - | - | - | - | To update | -https://cran.r-project.org/web/packages/spocc/index.html | -Ecology | -spocc_occ | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc | -1.2.2 | -- | - | - | - | 0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -56 | -769 | -- |
- | srs_tools | -srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata | -Compute biodiversity indicators for remote sensing data from Sentinel 2 | -- | - | - | - | - | - | - | To update | -- | Ecology | -- | ecology | -https://github.com/Marie59/Sentinel_2A/srs_tools | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools | -0.0.1 | -r-base | -- | - | - | 4 | -0 | -7 | -7 | -4 | -0 | -7 | -7 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -7 | -0 | -21 | -225 | -- |
- | stoc | -stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic | -Tools to analyse STOC data. | -- | - | - | - | - | - | - | To update | -- | Ecology | -stoceps | -ecology | -https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc | -0.0.2 | -- | - | - | - | 0 | -0 | -5 | -5 | -0 | -0 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -10 | -325 | -- |
- | taxonomy_filter_refseq | -taxonomy_filter_refseq | -Filter RefSeq by taxonomy | -- | - | - | - | - | - | - | To update | -https://github.com/pvanheus/ncbitaxonomy | -Sequence Analysis, Genome annotation | -taxonomy_filter_refseq | -iuc | -https://github.com/galaxyproject/tools-iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq | -0.3.0 | -rust-ncbitaxonomy | -1.0.7 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | taxonomy_krona_chart | -taxonomy_krona_chart | -Krona pie chart from taxonomic profile | -krona | -krona | -- | Krona | -Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). | -Visualisation | -Metagenomics | -To update | -http://sourceforge.net/projects/krona/ | -Assembly | -taxonomy_krona_chart | -crs4 | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart | -2.7.1+galaxy0 | -krona | -2.8.1 | -Visualisation | -Metagenomics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -1 | -1801 | -27426 | -- |
- | telescope | -telescope_assign | -Single locus resolution of Transposable ELEment expression. | -Telescope-expression | -Telescope-expression | -- | Telescope | -Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. | -Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping | -RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly | -Up-to-date | -https://github.com/mlbendall/telescope/ | -Genome annotation | -telescope_assign | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope | -1.0.3 | -telescope | -1.0.3 | -Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping | -RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | tgsgapcloser | -tgsgapcloser | -TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. | -TGS-GapCloser | -TGS-GapCloser | -- | TGS-GapCloser | -TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. | -Genome assembly, Read mapping, Scaffolding, Localised reassembly | -Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping | -To update | -https://github.com/BGI-Qingdao/TGS-GapCloser | -Assembly | -tgsgapcloser | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser | -https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser | -1.0.3 | -tgsgapcloser | -1.2.1 | -Genome assembly, Read mapping, Scaffolding, Localised reassembly | -Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -36 | -460 | -- |
- | transit | -gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps | -TRANSIT | -transit | -transit | -- | TRANSIT | -A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. | -Transposon prediction | -DNA, Sequencing, Mobile genetic elements | -To update | -https://github.com/mad-lab/transit/ | -Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit | -3.0.2 | -transit | -3.2.3 | -Transposon prediction | -DNA, Sequencing, Mobile genetic elements | -5 | -5 | -5 | -0 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -84 | -907 | -- |
- | trycycler | -trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample | -Trycycler toolkit wrappers | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/rrwick/Trycycler | -Assembly | -trycycler | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler | -0.5.5 | -trycycler | -0.5.5 | -- | - | 0 | -5 | -5 | -5 | -0 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -147 | -8942 | -- |
- | tsebra | -tsebra | -This tool has been developed to combine BRAKER predictions. | -tsebra | -tsebra | -- | TSEBRA | -TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. | -Homology-based gene prediction, Alternative splicing prediction | -Gene expression, RNA-Seq, Gene transcripts, Model organisms | -To update | -https://github.com/Gaius-Augustus/TSEBRA | -Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra | -1.1.2.4 | -tsebra | -1.1.2.5 | -Homology-based gene prediction, Alternative splicing prediction | -Gene expression, RNA-Seq, Gene transcripts, Model organisms | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -- |
- | unicycler | -unicycler | -Unicycler is a hybrid assembly pipeline for bacterial genomes. | -unicycler | -unicycler | -- | Unicycler | -A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. | -Genome assembly, Aggregation | -Microbiology, Genomics, Sequencing, Sequence assembly | -Up-to-date | -https://github.com/rrwick/Unicycler | -Assembly | -unicycler | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler | -0.5.0 | -unicycler | -0.5.0 | -Genome assembly, Aggregation | -Microbiology, Genomics, Sequencing, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1558 | -65732 | -- |
- | velvet | -velvetg, velveth | -de novo genomic assembler specially designed for short read sequencing technologies | -velvet | -velvet | -- | Velvet | -A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. | -Formatting, De-novo assembly | -Sequence assembly | -To update | -https://www.ebi.ac.uk/~zerbino/velvet/ | -Assembly | -velvet | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet | -- | velvet | -1.2.10 | -Formatting, De-novo assembly | -Sequence assembly | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -2083 | -25420 | -- |
- | velvet_optimiser | -velvetoptimiser | -Automatically optimize Velvet assemblies | -velvetoptimiser | -velvetoptimiser | -- | VelvetOptimiser | -This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. | -Optimisation and refinement, Sequence assembly | -Genomics, Sequence assembly | -To update | -- | Assembly | -velvetoptimiser | -simon-gladman | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser | -2.2.6+galaxy2 | -velvet | -1.2.10 | -Optimisation and refinement, Sequence assembly | -Genomics, Sequence assembly | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -255 | -4741 | -- |
- | verkko | -verkko | -Telomere-to-telomere assembly pipeline | -- | - | - | - | - | - | - | To update | -https://github.com/marbl/verkko | -Assembly | -verkko | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko | -1.3.1 | -verkko | -2.1 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -9 | -22 | -- |
- | vigiechiro | -vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid | -Tools created by the vigiechiro team to analyses and identify chiro sounds files. | -- | - | - | - | - | - | - | To update | -https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro | -Ecology | -vigiechiro | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro | -0.1.1 | -- | - | - | - | 0 | -0 | -4 | -4 | -0 | -0 | -4 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -4 | -351 | -12203 | -- |
- | wtdbg | -wtdbg | -WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. | -wtdbg2 | -wtdbg2 | -- | wtdbg2 | -Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. | -Genome assembly, De-novo assembly | -Sequence assembly, Sequencing | -Up-to-date | -https://github.com/ruanjue/wtdbg2 | -Assembly | -wtdbg | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg | -https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg | -2.5 | -wtdbg | -2.5 | -Genome assembly, De-novo assembly | -Sequence assembly, Sequencing | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -116 | -1660 | -- |
- | xarray | -timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select | -xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. | -- | - | - | - | - | - | - | To update | -http://xarray.pydata.org | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray | -2022.3.0 | -xarray | -- | - | - | 5 | -2 | -6 | -5 | -5 | -2 | -6 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -2 | -175 | -5876 | -- |
- | yahs | -yahs | -Yet Another Hi-C scaffolding tool | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/c-zhou/yahs | -Assembly | -yahs | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs | -1.2a.2 | -yahs | -1.2a.2 | -- | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -64 | -344 | -- |
- | zoo_project_ogc_api_processes | -zoo_project_ogc_api_processes | -This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. | -- | - | - | - | - | - | - | To update | -https://github.com/AquaINFRA/galaxy | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes | -0.1.0 | -r-base | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
Expand | -Galaxy wrapper id | -Galaxy tool ids | -Description | -bio.tool id | -bio.tool ids | -biii | -bio.tool name | -bio.tool description | -EDAM operation | -EDAM topic | -Status | -Source | -ToolShed categories | -ToolShed id | -Galaxy wrapper owner | -Galaxy wrapper source | -Galaxy wrapper parsed folder | -Galaxy wrapper version | -Conda id | -Conda version | -EDAM operation (no superclasses) | -EDAM topic (no superclasses) | -Available on UseGalaxy.org (Main) | -Available on UseGalaxy.org.au | -Available on UseGalaxy.eu | -Available on UseGalaxy.fr | -Tools available on UseGalaxy.org (Main) | -Tools available on UseGalaxy.org.au | -Tools available on UseGalaxy.eu | -Tools available on UseGalaxy.fr | -Tools available on ANASTASIA | -Tools available on APOSTL | -Tools available on ARGs-OAP | -Tools available on BF2I-MAP | -Tools available on BioBix | -Tools available on CIRM-CFBP | -Tools available on Center for Phage Technology (CPT) | -Tools available on ChemFlow | -Tools available on Coloc-stats | -Tools available on CorGAT | -Tools available on CropGalaxy | -Tools available on Dintor | -Tools available on FreeBioinfo | -Tools available on GASLINI | -Tools available on Galaxy@AuBi | -Tools available on Galaxy@Pasteur | -Tools available on GalaxyTrakr | -Tools available on Genomic Hyperbrowser | -Tools available on GigaGalaxy | -Tools available on HyPhy HIV NGS Tools | -Tools available on IPK Galaxy Blast Suite | -Tools available on ImmPort Galaxy | -Tools available on InteractoMIX | -Tools available on MISSISSIPPI | -Tools available on Mandoiu Lab | -Tools available on MiModD NacreousMap | -Tools available on Oqtans | -Tools available on Palfinder | -Tools available on PepSimili | -Tools available on PhagePromotor | -Tools available on Protologger | -Tools available on UseGalaxy.be | -Tools available on UseGalaxy.cz | -Tools available on UseGalaxy.no | -No. of tool users (2022-2023) (usegalaxy.eu) | -Total tool usage (usegalaxy.eu) | -Deprecated | -
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- | bia-ftplinks | -bia_download | -Tool to query ftp links for study from bioimage archive | -- | - | - | - | - | - | - | To update | -- | Imaging | -bia_download | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools | -https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks | -0.1.0 | -wget | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -- |
- | cellpose | -cellpose | -Cellpose is an anatomical segmentation algorithm | -- | - | - | - | - | - | - | To update | -https://github.com/MouseLand/cellpose | -Imaging | -cellpose | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/cellpose | -https://github.com/bgruening/galaxytools/tree/master/tools/cellpose | -3.0.8 | -cellpose | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | cellprofiler | -cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects | -cellProfiler wrapper | -CellProfiler | -CellProfiler | -cellprofiler | -CellProfiler | -Tool for quantifying data from biological images, particularly in high-throughput experiments. | -Quantification, Image analysis, Parsing | -Imaging, Microarray experiment, Genotype and phenotype | -To update | -- | Imaging | -cellprofiler | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools | -https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler | -- | - | - | Quantification, Image analysis, Parsing | -Imaging, Microarray experiment, Genotype and phenotype | -0 | -23 | -23 | -19 | -0 | -23 | -23 | -19 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -23 | -19 | -178 | -4614 | -- |
- | cellprofiler_v4 | -cp_cellprofiler4 | -cellProfiler4 wrapper | -- | - | - | - | - | - | - | To update | -- | Imaging | -cellprofiler4 | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools | -https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 | -4.2.6 | -- | - | - | - | 0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -8 | -43 | -- |
- | graphicsmagick | -graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage | -Contains tools based on GraphicsMagick | -- | - | - | - | - | - | - | To update | -http://www.graphicsmagick.org | -Imaging | -graphicsmagick | -bgruening | -https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ | -https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick | -1.3.43 | -graphicsmagick | -1.3.26 | -- | - | 1 | -0 | -3 | -0 | -1 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -43 | -2605 | -- |
- | hyperstack_to_bleach_corrected_movie | -hyperstack_to_bleach_corrected_movie | -Generate blach corrected movie from hyperstack | -- | - | - | - | - | - | - | To update | -- | Imaging | -hyperstack_to_bleach_corrected_movie | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie | -20230328 | -Fiji | -20231211 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | imagej2 | -imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary | -ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. | -imagej | -imagej | -imagej2 | -ImageJ2 | -It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. | -Image analysis, Image annotation, Visualisation | -Imaging | -To update | -http://fiji.sc | -Imaging | -imagej2 | -imgteam | -https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 | -https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 | -- | - | - | Image analysis, Image annotation, Visualisation | -Imaging | -0 | -0 | -27 | -0 | -0 | -0 | -27 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -27 | -27 | -26 | -1537 | -- |
- | incucyte_stack_and_upload_omero | -incucyte_stack_and_upload_omero | -Combine images to stack and upload to the omero server | -- | - | - | - | - | - | - | To update | -- | Imaging | -incucyte_stack_and_upload_omero | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero | -20231221 | -Fiji | -20231211 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | measure_gastruloids | -measureGastruloids | -Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index | -- | - | - | - | - | - | - | To update | -- | Imaging | -measure_gastruloids | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids | -20221216 | -fiji | -20231211 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | omero_clean_rois_tables | -omero_clean_rois_tables | -Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down | -- | - | - | - | - | - | - | To update | -- | Imaging | -omero_clean_rois_tables | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables | -20230623 | -fiji | -20231211 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | omero_get_children_ids | -omero_get_children_ids | -Get omero id of children of an omero object id | -- | - | - | - | - | - | - | To update | -- | Imaging | -omero_get_children_ids | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids | -0.2.0 | -omero-py | -5.11.1 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | omero_get_full_images | -omero_get_full_images | -Get full images from omero | -- | - | - | - | - | - | - | To update | -- | Imaging | -omero_get_full_images | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images | -20240521 | -fiji | -20231211 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | omero_hyperstack_to_fluo_measurements_on_gastruloid | -omero_hyperstack_to_fluo_measurements_on_gastruloid | -Analyse Hyperstack on OMERO server to measure fluorescence levels | -- | - | - | - | - | - | - | To update | -- | Imaging | -omero_hyperstack_to_fluo_measurements_on_gastruloid | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid | -20230809 | -fiji | -20231211 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | omero_hyperstack_to_gastruloid_measurements | -omero_hyperstack_to_gastruloid_measurements | -Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements | -- | - | - | - | - | - | - | To update | -- | Imaging | -omero_hyperstack_to_gastruloid_measurements | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements | -20240214 | -fiji | -20231211 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | qupath_roi_splitter | -qupath_roi_splitter | -Split ROI coordinates of QuPath TMA annotation by cell type | -- | - | - | - | - | - | - | To update | -https://github.com/npinter/ROIsplitter | -Imaging | -qupath_roi_splitter | -galaxyp | -hhttps://github.com/npinter/ROIsplitter | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter | -0.2.1 | -geojson | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -5 | -59 | -- |
- | spyboat | -spyboat | -Wavelet analysis for 3d-image stacks | -- | - | - | - | - | - | - | To update | -http://github.com/tensionhead/spyboat | -Imaging, Graphics | -spyboat | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat | -0.1.2 | -spyboat | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -67 | -- |
- | upload_roi_and_measures_to_omero | -uploadROIandMeasuresToOMERO | -Upload the ROI coordinates and the measurements to the omero server | -- | - | - | - | - | - | - | To update | -- | Imaging | -upload_roi_and_measures_to_omero | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero | -0.0.5 | -omero-py | -5.11.1 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | woundhealing | -woundhealing_scratch_assay | -Tool to automate quantification of wound healing in high-throughput microscopy scratch assays | -- | - | - | - | - | - | - | Up-to-date | -https://git.embl.de/grp-cba/wound-healing-htm-screen | -Imaging | -Wound healing scratch assay image analysis | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools | -https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing | -1.6.1 | -fiji-morpholibj | -1.6.1 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
Expand | -Galaxy wrapper id | -Galaxy tool ids | -Description | -bio.tool id | -bio.tool ids | -biii | -bio.tool name | -bio.tool description | -EDAM operation | -EDAM topic | -Status | -Source | -ToolShed categories | -ToolShed id | -Galaxy wrapper owner | -Galaxy wrapper source | -Galaxy wrapper parsed folder | -Galaxy wrapper version | -Conda id | -Conda version | -EDAM operation (no superclasses) | -EDAM topic (no superclasses) | -Available on UseGalaxy.org (Main) | -Available on UseGalaxy.org.au | -Available on UseGalaxy.eu | -Available on UseGalaxy.fr | -Tools available on UseGalaxy.org (Main) | -Tools available on UseGalaxy.org.au | -Tools available on UseGalaxy.eu | -Tools available on UseGalaxy.fr | -Tools available on ANASTASIA | -Tools available on APOSTL | -Tools available on ARGs-OAP | -Tools available on BF2I-MAP | -Tools available on BioBix | -Tools available on CIRM-CFBP | -Tools available on Center for Phage Technology (CPT) | -Tools available on ChemFlow | -Tools available on Coloc-stats | -Tools available on CorGAT | -Tools available on CropGalaxy | -Tools available on Dintor | -Tools available on FreeBioinfo | -Tools available on GASLINI | -Tools available on Galaxy@AuBi | -Tools available on Galaxy@Pasteur | -Tools available on GalaxyTrakr | -Tools available on Genomic Hyperbrowser | -Tools available on GigaGalaxy | -Tools available on HyPhy HIV NGS Tools | -Tools available on IPK Galaxy Blast Suite | -Tools available on ImmPort Galaxy | -Tools available on InteractoMIX | -Tools available on MISSISSIPPI | -Tools available on Mandoiu Lab | -Tools available on MiModD NacreousMap | -Tools available on Oqtans | -Tools available on Palfinder | -Tools available on PepSimili | -Tools available on PhagePromotor | -Tools available on Protologger | -Tools available on UseGalaxy.be | -Tools available on UseGalaxy.cz | -Tools available on UseGalaxy.no | -No. of tool users (2022-2023) (usegalaxy.eu) | -Total tool usage (usegalaxy.eu) | -Deprecated | -
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
- | biomodelsML | -biomodels_biomd0000001066, biomodels_biomd0000001076 | -Wrappers for tools to bring BioModels AI models into Galaxy. | -- | - | - | - | - | - | - | To update | -https://www.ebi.ac.uk/biomodels/ | -Machine Learning | -biomodels | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools | -https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML | -1.1 | -- | - | - | - | 0 | -0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -13 | -- |
- | chopin2 | -chopin2 | -Domain-Agnostic Supervised Learning with Hyperdimensional Computing | -- | - | - | - | - | - | - | To update | -https://github.com/cumbof/chopin2 | -Machine Learning | -chopin2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 | -1.0.9.post1 | -chopin2 | -- | - | - | 1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | decontaminator | -decontaminator | -Deep Learning method for novel virus detection in sequencing data | -decontaminator | -decontaminator | -- | - | - | - | - | To update | -https://github.com/cbib/decontaminator | -Machine Learning | -decontaminator | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator | -1.0.0 | -numpy | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -15 | -99 | -- |
- | deepmicro | -deepmicro | -Representation learning and classification framework | -DeepMicro | -DeepMicro | -- | DeepMicro | -Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. | -Essential dynamics, Splitting, Community profiling | -Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics | -Up-to-date | -https://github.com/paulzierep/DeepMicro | -Machine Learning | -deepmicro | -iuc | -https://github.com/paulzierep/DeepMicro | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro | -1.4 | -deepmicro | -1.4 | -Essential dynamics, Splitting | -Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -3 | -501 | -- |
- | sklearn | -sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split | -Machine Learning tool suite from Scikit-learn | -- | - | - | - | - | - | - | To update | -http://scikit-learn.org | -Machine Learning, Statistics | -sklearn | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/sklearn | -https://github.com/bgruening/galaxytools/tree/master/tools/sklearn | -1.0.11.0 | -- | - | - | - | 30 | -14 | -31 | -16 | -30 | -14 | -31 | -16 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -31 | -27 | -958 | -113932 | -- |
- | tool_recommendation_model | -create_tool_recommendation_model | -Create model to recommend tools | -- | - | - | - | - | - | - | To update | -https://github.com/bgruening/galaxytools | -Machine Learning | -create_tool_recommendation_model | -bgruening | -https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model | -https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model | -0.0.5 | -python | -- | - | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -15 | -445 | -- |
- | virhunter | -virhunter | -Deep Learning method for novel virus detection in sequencing data | -virhunter | -virhunter | -- | VirHunter | -VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). | -Sequence classification | -Virology | -To update | -https://github.com/cbib/virhunter | -Machine Learning | -virhunter | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter | -1.0.0 | -numpy | -- | Sequence classification | -Virology | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -40 | -234 | -- |
- | whisper | -whisper | -Transcribe audio or video files to text using the OpenAI Whisper. | -- | - | - | - | - | - | - | To update | -https://github.com/bgruening/galaxytools/tree/master/tools/whisper | -Machine Learning | -whisper | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/whisper | -https://github.com/bgruening/galaxytools/tree/master/tools/whisper | -20231117 | -- | - | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
Expand | -Galaxy wrapper id | -Galaxy tool ids | -Description | -bio.tool id | -bio.tool ids | -biii | -bio.tool name | -bio.tool description | -EDAM operation | -EDAM topic | -Status | -Source | -ToolShed categories | -ToolShed id | -Galaxy wrapper owner | -Galaxy wrapper source | -Galaxy wrapper parsed folder | -Galaxy wrapper version | -Conda id | -Conda version | -EDAM operation (no superclasses) | -EDAM topic (no superclasses) | -Available on UseGalaxy.org (Main) | -Available on UseGalaxy.org.au | -Available on UseGalaxy.eu | -Available on UseGalaxy.fr | -Tools available on UseGalaxy.org (Main) | -Tools available on UseGalaxy.org.au | -Tools available on UseGalaxy.eu | -Tools available on UseGalaxy.fr | -Tools available on ANASTASIA | -Tools available on APOSTL | -Tools available on ARGs-OAP | -Tools available on BF2I-MAP | -Tools available on BioBix | -Tools available on CIRM-CFBP | -Tools available on Center for Phage Technology (CPT) | -Tools available on ChemFlow | -Tools available on Coloc-stats | -Tools available on CorGAT | -Tools available on CropGalaxy | -Tools available on Dintor | -Tools available on FreeBioinfo | -Tools available on GASLINI | -Tools available on Galaxy@AuBi | -Tools available on Galaxy@Pasteur | -Tools available on GalaxyTrakr | -Tools available on Genomic Hyperbrowser | -Tools available on GigaGalaxy | -Tools available on HyPhy HIV NGS Tools | -Tools available on IPK Galaxy Blast Suite | -Tools available on ImmPort Galaxy | -Tools available on InteractoMIX | -Tools available on MISSISSIPPI | -Tools available on Mandoiu Lab | -Tools available on MiModD NacreousMap | -Tools available on Oqtans | -Tools available on Palfinder | -Tools available on PepSimili | -Tools available on PhagePromotor | -Tools available on Protologger | -Tools available on UseGalaxy.be | -Tools available on UseGalaxy.cz | -Tools available on UseGalaxy.no | -No. of tool users (2022-2023) (usegalaxy.eu) | -Total tool usage (usegalaxy.eu) | -Deprecated | -
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
- | PAMPA | -pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm | -Tools to compute and analyse biodiversity metrics | -- | - | - | - | - | - | - | To update | -- | Ecology | -pampa | -ecology | -https://github.com/ColineRoyaux/PAMPA-Galaxy | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA | -0.0.2 | -- | - | - | - | 0 | -5 | -5 | -5 | -0 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -4 | -73 | -1004 | -False | -
- | TreeBest | -treebest_best | -TreeBeST best | -treebest | -treebest | -- | TreeBeST | -TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. | -Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) | -Phylogenetics | -To update | -http://treesoft.sourceforge.net/treebest.shtml | -Phylogenetics | -treebest_best | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest | -1.9.2.post0 | -treebest | -1.9.2.post1 | -Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) | -Phylogenetics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -23 | -984 | -False | -
- | abacas | -abacas | -Order and Orientate Contigs | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/abacas | -Assembly | -abacas | -nml | -https://github.com/phac-nml/abacas | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas | -1.1 | -mummer | -3.23 | -- | - | 0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | abricate | -abricate, abricate_list, abricate_summary | -Mass screening of contigs for antiobiotic resistance genes | -ABRicate | -ABRicate | -- | ABRicate | -Mass screening of contigs for antimicrobial resistance or virulence genes. | -Antimicrobial resistance prediction | -Genomics, Microbiology | -Up-to-date | -https://github.com/tseemann/abricate | -Sequence Analysis | -abricate | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate | -1.0.1 | -abricate | -1.0.1 | -Antimicrobial resistance prediction | -Genomics, Microbiology | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -1764 | -496717 | -False | -
- | abritamr | -abritamr | -A pipeline for running AMRfinderPlus and collating results into functional classes | -abritamr | -abritamr | -- | abriTAMR | -an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. | -Antimicrobial resistance prediction | -Microbiology, Public health and epidemiology, Infectious disease | -To update | -https://zenodo.org/record/7370628 | -Sequence Analysis | -abritamr | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr | -1.0.14 | -abritamr | -1.0.18 | -Antimicrobial resistance prediction | -Microbiology, Public health and epidemiology, Infectious disease | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | abyss | -abyss-pe | -Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler | -abyss | -abyss | -- | ABySS | -De novo genome sequence assembler using short reads. | -Genome assembly, De-novo assembly, Scaffolding | -Sequence assembly | -Up-to-date | -http://www.bcgsc.ca/platform/bioinfo/software/abyss | -Assembly | -abyss | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss | -2.3.7 | -abyss | -2.3.7 | -Genome assembly, De-novo assembly, Scaffolding | -Sequence assembly | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -391 | -4278 | -False | -
- | aldex2 | -aldex2 | -Performs analysis Of differential abundance taking sample variation into account | -aldex2 | -aldex2 | -- | ALDEx2 | -A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. | -Statistical inference | -Gene expression, Statistics and probability | -To update | -https://github.com/ggloor/ALDEx_bioc | -Metagenomics | -aldex2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 | -1.26.0 | -bioconductor-aldex2 | -1.34.0 | -Statistical inference | -Gene expression, Statistics and probability | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -13 | -129 | -False | -
- | amplican | -amplican | -AmpliCan is an analysis tool for genome editing. | -amplican | -amplican | -- | amplican | -It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. | -Alignment, Standardisation and normalisation | -PCR experiment, Statistics and probability | -To update | -https://github.com/valenlab/amplican | -Sequence Analysis | -amplican | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican | -1.14.0 | -bioconductor-amplican | -1.24.0 | -Alignment, Standardisation and normalisation | -PCR experiment, Statistics and probability | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -12 | -53 | -False | -
- | amrfinderplus | -amrfinderplus | -"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. | -amrfinderplus | -amrfinderplus | -- | AMRFinderPlus | -AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms | -Antimicrobial resistance prediction | -Microbiology, Public health and epidemiology, Infectious disease | -Up-to-date | -https://github.com/ncbi/amr | -Sequence Analysis | -AMRFinderPlus | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus | -3.12.8 | -ncbi-amrfinderplus | -3.12.8 | -Antimicrobial resistance prediction | -Microbiology, Public health and epidemiology, Infectious disease | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -591 | -False | -
- | ancombc | -ancombc | -Performs analysis of compositions of microbiomes with bias correction. | -ancombc | -ancombc | -- | ANCOMBC | -Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. | -DNA barcoding | -Microbial ecology, Metagenomics, Taxonomy | -To update | -https://github.com/FrederickHuangLin/ANCOMBC | -Metagenomics | -ancombc | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc | -1.4.0 | -bioconductor-ancombc | -2.4.0 | -DNA barcoding | -Microbial ecology, Metagenomics, Taxonomy | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -4 | -7 | -False | -
- | antismash | -antismash | -Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters | -antismash | -antismash | -- | antiSMASH | -Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. | -Sequence clustering, Gene prediction, Differential gene expression analysis | -Molecular interactions, pathways and networks, Gene and protein families | -To update | -https://antismash.secondarymetabolites.org | -Sequence Analysis | -antismash | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash | -https://github.com/bgruening/galaxytools/tree/master/tools/antismash | -6.1.1 | -antismash | -7.1.0 | -Sequence clustering, Gene prediction, Differential gene expression analysis | -Molecular interactions, pathways and networks, Gene and protein families | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -279 | -14596 | -False | -
- | artic | -artic_guppyplex, artic_minion | -The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building | -artic | -artic | -- | ARTIC | -A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore | -Sequence alignment | -Genomics | -To update | -https://github.com/artic-network/fieldbioinformatics | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic | -- | artic | -1.2.4 | -Sequence alignment | -Genomics | -0 | -0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -1 | -123 | -8175 | -False | -
- | assemblystats | -assemblystats | -Summarise an assembly (e.g. N50 metrics) | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools | -Assembly | -assemblystats | -nml | -https://github.com/phac-nml/galaxy_tools | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats | -1.1.0 | -perl-bioperl | -1.7.8 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | bakta | -bakta | -"Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." | -bakta | -bakta | -- | Bakta | -Rapid & standardized annotation of bacterial genomes, MAGs & plasmids | -Genome annotation | -Genomics, Data submission, annotation and curation, Sequence analysis | -To update | -https://github.com/oschwengers/bakta | -Sequence Analysis | -bakta | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta | -1.9.3 | -bakta | -- | Genome annotation | -Genomics, Data submission, annotation and curation, Sequence analysis | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -151 | -2982 | -False | -
- | bamtools | -bamtools | -Operate on and transform BAM datasets in various ways using bamtools | -bamtools | -bamtools | -- | BamTools | -BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. | -Data handling, Sequence alignment analysis | -Sequencing, Data management, Sequence analysis | -Up-to-date | -https://github.com/pezmaster31/bamtools | -Sequence Analysis, SAM | -bamtools | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools | -2.5.2 | -bamtools | -2.5.2 | -Data handling, Sequence alignment analysis | -Sequencing, Sequence analysis | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -208 | -14021 | -False | -
- | bandage | -bandage_image, bandage_info | -Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily | -bandage | -bandage | -- | Bandage | -GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. | -Sequence assembly visualisation | -Genomics, Sequence assembly | -Up-to-date | -https://github.com/rrwick/Bandage | -Visualization | -bandage | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage | -2022.09 | -bandage_ng | -2022.09 | -Sequence assembly visualisation | -Genomics, Sequence assembly | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -2016 | -44390 | -False | -
- | bayescan | -BayeScan | -Detecting natural selection from population-based genetic data | -bayescan | -bayescan | -- | BayeScan | -BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. | -Statistical inference | -Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism | -To update | -http://cmpg.unibe.ch/software/BayeScan/index.html | -Sequence Analysis | -bayescan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan | -2.1 | -bayescan | -2.0.1 | -Statistical inference | -Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -8 | -64 | -False | -
- | bbtools | -bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole | -BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. | -bbmap | -bbtools, bbmap | -- | BBMap | -BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. | -RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment | -Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq | -Up-to-date | -https://jgi.doe.gov/data-and-tools/bbtools/ | -Sequence Analysis | -bbtools | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools | -39.06 | -bbmap | -39.06 | -RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment | -RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq | -6 | -1 | -5 | -0 | -6 | -1 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -420 | -6381 | -False | -
- | bigscape | -bigscape | -Construct sequence similarity networks of BGCs and groups them into GCF | -BiG-SCAPE | -BiG-SCAPE | -- | BiG-SCAPE | -A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. | -Clustering, Global alignment, Fold recognition | -Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families | -Up-to-date | -https://github.com/medema-group/BiG-SCAPE | -Metagenomics | -bigscape | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape | -1.1.9 | -bigscape | -1.1.9 | -Clustering, Global alignment, Fold recognition | -Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | binning_refiner | -bin_refiner | -Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. | -binning_refiner | -binning_refiner | -- | Binning_refiner | -Improving genome bins through the combination of different binning programs | -Read binning, Sequence clustering | -Metagenomics, Sequence assembly, Microbial ecology | -Up-to-date | -https://github.com/songweizhi/Binning_refiner | -Metagenomics | -binning_refiner | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner | -1.4.3 | -binning_refiner | -1.4.3 | -Read binning, Sequence clustering | -Metagenomics, Sequence assembly, Microbial ecology | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -21 | -81 | -False | -
- | biohansel | -biohansel | -Heidelberg and Enteritidis SNP Elucidation | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/biohansel | -Sequence Analysis | -biohansel | -nml | -https://github.com/phac-nml/biohansel | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel | -2.4.0 | -bio_hansel | -2.6.1 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | biom_format | -biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table | -The biom-format package provides a command line interface and Python API for working with BIOM files. | -biomformat | -biomformat | -- | biomformat | -This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. | -Formatting | -Laboratory information management, Sequence analysis | -To update | -https://github.com/biocore/biom-format | -Metagenomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format | -2.1.15 | -biom-format | -2.1.7 | -Formatting | -Laboratory information management, Sequence analysis | -2 | -2 | -6 | -0 | -2 | -2 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -98 | -3906 | -False | -
- | biotradis | -bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites | -Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. | -biotradis | -biotradis | -- | biotradis | -The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. | -Sequence analysis | -Mobile genetic elements, Workflows | -Up-to-date | -https://www.sanger.ac.uk/science/tools/bio-tradis | -Genome annotation | -biotradis | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis | -1.4.5 | -biotradis | -1.4.5 | -Sequence analysis | -Mobile genetic elements, Workflows | -3 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | blast2go | -blast2go | -Maps BLAST results to GO annotation terms | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go | -Ontology Manipulation, Sequence Analysis | -blast2go | -peterjc | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go | -0.0.11 | -b2g4pipe | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -101 | -1232 | -False | -
- | blast_rbh | -blast_reciprocal_best_hits | -BLAST Reciprocal Best Hits (RBH) from two FASTA files | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | -Fasta Manipulation, Sequence Analysis | -blast_rbh | -peterjc | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | -0.3.0 | -biopython | -1.70 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -121 | -22499 | -False | -
- | blastxml_to_top_descr | -blastxml_to_top_descr | -Make table of top BLAST match descriptions | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr | -Convert Formats, Sequence Analysis, Text Manipulation | -blastxml_to_top_descr | -peterjc | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr | -0.1.2 | -python | -- | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -159 | -264558 | -False | -
- | bracken | -est_abundance | -Bayesian Reestimation of Abundance with KrakEN | -bracken | -bracken | -- | Bracken | -Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. | -Statistical calculation | -Metagenomics, Microbial ecology | -Up-to-date | -https://ccb.jhu.edu/software/bracken/ | -Sequence Analysis, Metagenomics | -bracken | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken | -2.9 | -bracken | -2.9 | -Statistical calculation | -Metagenomics, Microbial ecology | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -326 | -18351 | -False | -
- | busco | -busco | -BUSCO assess genome and annotation completeness | -busco | -busco | -- | BUSCO | -Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. | -Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly | -Sequence assembly, Genomics, Transcriptomics, Sequence analysis | -To update | -https://gitlab.com/ezlab/busco/-/releases | -Sequence Analysis | -busco | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco | -5.5.0 | -busco | -5.7.1 | -Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly | -Sequence assembly, Transcriptomics, Sequence analysis | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1804 | -86180 | -False | -
- | cat | -cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise | -Contig Annotation Tool (CAT) | -cat_bins | -cat_bins | -- | CAT and BAT | -Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. | -Taxonomic classification, Sequence assembly, Coding region prediction | -Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly | -To update | -https://github.com/dutilh/CAT | -Metagenomics | -contig_annotation_tool | -iuc | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat | -5.2.3 | -cat | -5.3 | -Taxonomic classification, Sequence assembly, Coding region prediction | -Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly | -5 | -2 | -5 | -0 | -5 | -2 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -268 | -2878 | -False | -
- | cd_hit_dup | -cd_hit_dup | -simple tool for removing duplicates from sequencing reads | -- | - | - | - | - | - | - | To update | -- | Metagenomics, Sequence Analysis | -cd_hit_dup | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup | -0.0.1 | -cd-hit-auxtools | -4.8.1 | -- | - | 1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | cdhit | -cd_hit | -Cluster or compare biological sequence datasets | -cd-hit | -cd-hit | -- | cd-hit | -Cluster a nucleotide dataset into representative sequences. | -Sequence clustering | -Sequencing | -Up-to-date | -http://weizhongli-lab.org/cd-hit/ | -Sequence Analysis, Fasta Manipulation | -cd_hit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit | -4.8.1 | -cd-hit | -4.8.1 | -Sequence clustering | -Sequencing | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -280 | -4474 | -False | -
- | cemitool | -cemitool | -Gene co-expression network analysis tool | -cemitool | -cemitool | -- | CEMiTool | -It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. | -Enrichment analysis, Pathway or network analysis | -Gene expression, Transcriptomics, Microarray experiment | -To update | -https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html | -Transcriptomics, RNA, Statistics | -cemitool | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool | -1.18.1 | -bioconductor-cemitool | -1.26.0 | -Enrichment analysis, Pathway or network analysis | -Transcriptomics, Microarray experiment | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -9 | -98 | -False | -
- | checkm | -checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa | -Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes | -checkm | -checkm | -- | CheckM | -CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. | -Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation | -Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management | -To update | -https://github.com/Ecogenomics/CheckM | -Metagenomics | -checkm | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm | -1.2.0 | -checkm-genome | -1.2.2 | -Sequence assembly validation, Sequence composition calculation, Statistical calculation | -Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management | -0 | -0 | -10 | -10 | -0 | -0 | -10 | -10 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -10 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -10 | -0 | -390 | -5165 | -False | -
- | clair3 | -clair3 | -Symphonizing pileup and full-alignment for high-performance long-read variant calling | -clair3 | -clair3 | -- | Clair3 | -Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. | -Variant calling | -Molecular genetics | -To update | -https://github.com/HKU-BAL/Clair3 | -Sequence Analysis, Variant Analysis | -clair3 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 | -0.1.12 | -clair3 | -1.0.8 | -Variant calling | -Molecular genetics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -68 | -1856 | -False | -
- | clinod | -clinod | -NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins | -clinod | -clinod | -- | clinod | -The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. | -Nucleic acid sequence analysis | -Sequence analysis | -To update | -http://www.compbio.dundee.ac.uk/www-nod/ | -Sequence Analysis | -clinod | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod | -https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod | -0.1.0 | -clinod | -1.3 | -Nucleic acid sequence analysis | -Sequence analysis | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | clustalw | -clustalw | -ClustalW multiple sequence alignment program for DNA or proteins | -clustal2 | -clustal2 | -- | Clustal 2 (Clustal W, Clustal X) | -Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. | -Multiple sequence alignment | -Phylogeny, Sequence analysis | -Up-to-date | -http://www.clustal.org/clustal2/ | -Phylogenetics, Sequence Analysis | -clustalw | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw | -2.1 | -clustalw | -2.1 | -Multiple sequence alignment | -Phylogeny, Sequence analysis | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -651 | -46793 | -False | -
- | cmsearch_deoverlap | -cmsearch_deoverlap | -removes lower scoring overlaps from cmsearch results. | -cmsearch-deoverlap | -cmsearch-deoverlap | -- | cmsearch-deoverlap | -Removes lower scoring overlaps from cmsearch results. | -Comparison, Alignment | -Biology, Medicine | -To update | -https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl | -RNA | -cmsearch_deoverlap | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap | -0.08+galaxy2 | -perl | -- | Comparison, Alignment | -Biology, Medicine | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -102 | -False | -
- | codeml | -codeml | -Detects positive selection | -paml | -paml | -- | PAML | -Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. | -Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis | -Phylogenetics, Sequence analysis | -To update | -http://abacus.gene.ucl.ac.uk/software/paml.html | -Phylogenetics | -codeml | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml | -4.9 | -paml | -4.10.7 | -Probabilistic sequence generation | -Phylogenetics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -29 | -60901 | -False | -
- | cojac | -cooc_mutbamscan, cooc_pubmut, cooc_tabmut | -co-occurrence of mutations on amplicons | -cojac | -cojac | -- | COJAC | -CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. | -- | Genetic variation | -Up-to-date | -https://github.com/cbg-ethz/cojac | -Metagenomics, Sequence Analysis | -cojac | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac | -0.9.2 | -cojac | -0.9.2 | -- | Genetic variation | -2 | -0 | -3 | -0 | -2 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -20 | -2757 | -False | -
- | combine_assembly_stats | -combine_stats | -Combine multiple Assemblystats datasets into a single tabular report | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools | -Assembly | -combine_assemblystats | -nml | -https://github.com/phac-nml/galaxy_tools | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats | -1.0 | -perl-getopt-long | -2.58 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | combine_metaphlan_humann | -combine_metaphlan_humann | -Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances | -combine_metaphlan_and_humann | -combine_metaphlan_and_humann | -- | Combine Metaphlan and HUMAnN | -This tool combine MetaPhlAn outputs and HUMANnN outputs | -Aggregation | -Metagenomics, Molecular interactions, pathways and networks | -To update | -- | Metagenomics | -combine_metaphlan2_humann2 | -bebatut | -https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 | -https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann | -0.3.0 | -python | -- | Aggregation | -Metagenomics, Molecular interactions, pathways and networks | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -9 | -147 | -False | -
- | compare_humann2_output | -compare_humann2_output | -Compare outputs of HUMAnN2 for several samples and extract similar and specific information | -compare_humann2_outputs | -compare_humann2_outputs | -- | Compare HUMAnN2 outputs | -This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples | -Comparison | -Metagenomics, Gene and protein families | -To update | -- | Metagenomics | -compare_humann2_output | -bebatut | -https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output | -https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output | -0.2.0 | -- | - | Comparison | -Metagenomics, Gene and protein families | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -10 | -332 | -False | -
- | compleasm | -compleasm | -Compleasm: a faster and more accurate reimplementation of BUSCO | -compleasm | -compleasm | -- | compleasm | -"Compleasm: a faster and more accurate reimplementation of BUSCO" | -Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly | -Sequence assembly, Genomics, Transcriptomics, Sequence analysis | -Up-to-date | -https://github.com/huangnengCSU/compleasm | -Sequence Analysis | -compleasm | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm | -0.2.6 | -compleasm | -0.2.6 | -Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly | -Sequence assembly, Transcriptomics, Sequence analysis | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | concoct | -concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering | -CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. | -concoct | -concoct | -- | CONCOCT | -A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. | -Sequence clustering, Read binning | -Metagenomics | -Up-to-date | -https://github.com/BinPro/CONCOCT | -Metagenomics | -concoct | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct | -1.1.0 | -concoct | -1.1.0 | -Sequence clustering, Read binning | -Metagenomics | -0 | -0 | -5 | -5 | -0 | -0 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -92 | -786 | -False | -
- | coverm | -coverm_contig, coverm_genome | -CoverM genome and contig wrappers | -coverm | -coverm | -- | CoverM | -Read coverage calculator for metagenomics | -Local alignment | -Bioinformatics | -Up-to-date | -https://github.com/wwood/CoverM | -Sequence Analysis | -coverm | -iuc | -https://github.com/galaxyproject/tools-iuc/tools/coverm | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm | -0.7.0 | -coverm | -0.7.0 | -Local alignment | -Bioinformatics | -0 | -0 | -2 | -2 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -72 | -529 | -False | -
- | cryptogenotyper | -CryptoGenotyper | -CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/phac-nml/CryptoGenotyper | -Sequence Analysis | -cryptogenotyper | -nml | -https://github.com/phac-nml/CryptoGenotyper | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper | -1.0 | -cryptogenotyper | -1.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -16 | -8518 | -False | -
- | cutadapt | -cutadapt | -Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). | -cutadapt | -cutadapt | -- | Cutadapt | -Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. | -Sequence trimming, Primer removal, Read pre-processing | -Genomics, Probes and primers, Sequencing | -To update | -https://cutadapt.readthedocs.org/en/stable/ | -Fasta Manipulation, Fastq Manipulation, Sequence Analysis | -cutadapt | -lparsons | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt | -4.8 | -cutadapt | -4.9 | -Sequence trimming, Primer removal, Read pre-processing | -Genomics, Probes and primers, Sequencing | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -1 | -5090 | -232004 | -False | -
- | dada2 | -dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts | -DADA2 wrappers | -dada2 | -dada2 | -- | dada2 | -This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. | -Variant calling, DNA barcoding | -Sequencing, Genetic variation, Microbial ecology, Metagenomics | -To update | -https://benjjneb.github.io/dada2/index.html | -Metagenomics | -dada2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 | -- | bioconductor-dada2 | -1.30.0 | -Variant calling, DNA barcoding | -Sequencing, Genetic variation, Microbial ecology, Metagenomics | -10 | -10 | -10 | -10 | -10 | -10 | -10 | -10 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -10 | -0 | -10 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -10 | -10 | -1263 | -66609 | -False | -
- | das_tool | -Fasta_to_Contig2Bin, das_tool | -DAS Tool for genome resolved metagenomics | -dastool | -dastool | -- | dastool | -DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. | -Read binning | -Metagenomics | -Up-to-date | -https://github.com/cmks/DAS_Tool | -Metagenomics | -das_tool | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool | -1.1.7 | -das_tool | -1.1.7 | -Read binning | -Metagenomics | -0 | -0 | -2 | -2 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -24 | -706 | -False | -
- | deseq2 | -deseq2 | -Differential gene expression analysis based on the negative binomial distribution | -DESeq2 | -DESeq2 | -- | DESeq2 | -R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. | -Differential gene expression analysis, RNA-Seq analysis | -RNA-Seq | -To update | -https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html | -Transcriptomics, RNA, Statistics | -deseq2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 | -2.11.40.8 | -bioconductor-deseq2 | -1.42.0 | -Differential gene expression analysis, RNA-Seq analysis | -RNA-Seq | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -1 | -4990 | -95752 | -False | -
- | diamond | -bg_diamond, bg_diamond_makedb, bg_diamond_view | -DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. | -diamond | -diamond | -- | Diamond | -Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. | -Sequence alignment analysis | -Sequence analysis, Proteins | -To update | -https://github.com/bbuchfink/diamond | -Sequence Analysis | -diamond | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond | -2.0.15 | -diamond | -2.1.9 | -Sequence alignment analysis | -Sequence analysis, Proteins | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -3 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -963 | -49711 | -False | -
- | disco | -disco | -DISCO is a overlap-layout-consensus (OLC) metagenome assembler | -disco | -disco | -- | DISCO | -DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. | -Protein sequence analysis | -Structure determination | -To update | -http://disco.omicsbio.org/ | -Metagenomics, Assembly | -disco | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco | -- | disco | -1.2 | -Protein sequence analysis | -Structure determination | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -42 | -369 | -False | -
- | dram | -dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer | -DRAM for distilling microbial metabolism to automate the curation of microbiome function | -dram | -dram | -- | DRAM | -Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes | -Gene functional annotation | -Metagenomics, Biological databases, Molecular genetics | -To update | -https://github.com/WrightonLabCSU/DRAM | -Metagenomics | -dram | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram | -1.3.5 | -dram | -1.5.0 | -Gene functional annotation | -Metagenomics, Biological databases, Molecular genetics | -0 | -0 | -5 | -0 | -0 | -0 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -39 | -6886 | -False | -
- | drep | -drep_compare, drep_dereplicate | -dRep compares and dereplicates genome sets | -drep | -drep | -- | dRep | -Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. | -Genome comparison | -Metagenomics, Genomics, Sequence analysis | -Up-to-date | -https://github.com/MrOlm/drep | -Metagenomics | -drep | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep | -3.5.0 | -drep | -3.5.0 | -Genome comparison | -Metagenomics, Sequence analysis | -0 | -0 | -2 | -2 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -46 | -646 | -False | -
- | ectyper | -ectyper | -EC-Typer - in silico serotyping of Escherichia coli species | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/phac-nml/ecoli_serotyping | -Sequence Analysis | -ectyper | -nml | -https://github.com/phac-nml/ecoli_serotyping | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper | -1.0.0 | -ectyper | -1.0.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -53 | -9907 | -False | -
- | effectiveT3 | -effectiveT3 | -Find bacterial type III effectors in protein sequences | -effectivet3 | -effectivet3 | -- | EffectiveT3 | -Prediction of putative Type-III secreted proteins. | -Sequence classification | -Sequence analysis | -To update | -http://effectors.org | -Sequence Analysis | -effectivet3 | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 | -https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 | -0.0.21 | -effectiveT3 | -1.0.1 | -Sequence classification | -Sequence analysis | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | eggnog_mapper | -eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search | -eggnog-mapper fast functional annotation of novel sequences | -eggnog-mapper-v2 | -eggnog-mapper-v2 | -- | eggNOG-mapper v2 | -EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. | -Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval | -Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis | -To update | -- | Proteomics | -eggnog_mapper | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper | -2.1.8 | -eggnog-mapper | -2.1.12 | -Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval | -Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -3 | -1 | -510 | -30565 | -False | -
- | emboss_5 | -EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 | -Galaxy wrappers for EMBOSS version 5.0.0 tools | -emboss | -emboss | -- | EMBOSS | -Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. | -Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment | -Molecular biology, Sequence analysis, Biology | -To update | -http://emboss.open-bio.org/ | -Sequence Analysis, Fasta Manipulation | -emboss_5 | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 | -5.0.0 | -emboss | -6.6.0 | -Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment | -Molecular biology, Sequence analysis | -107 | -107 | -107 | -107 | -107 | -107 | -107 | -107 | -0 | -0 | -0 | -0 | -0 | -0 | -107 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -107 | -0 | -0 | -107 | -0 | -0 | -0 | -107 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -107 | -107 | -1816 | -89530 | -False | -
- | ete | -ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator | -Analyse phylogenetic trees using the ETE Toolkit | -ete | -ete | -- | ete | -The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org | -Phylogenetic analysis, Phylogenetic tree editing | -Phylogenetics | -To update | -http://etetoolkit.org/ | -Phylogenetics | -ete | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete | -3.1.2 | -ete3 | -3.1.1 | -Phylogenetic tree editing | -Phylogenetics | -0 | -0 | -7 | -7 | -0 | -0 | -7 | -7 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -7 | -7 | -45 | -899 | -False | -
- | export2graphlan | -export2graphlan | -export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn | -export2graphlan | -export2graphlan | -- | export2graphlan | -export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. | -Conversion | -Taxonomy, Metabolomics, Biomarkers | -To update | -https://bitbucket.org/CibioCM/export2graphlan/overview | -Metagenomics | -export2graphlan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan | -0.20 | -export2graphlan | -0.22 | -Conversion | -Taxonomy, Metabolomics, Biomarkers | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -200 | -5265 | -False | -
- | ez_histograms | -ez_histograms | -ggplot2 histograms and density plots | -- | - | - | - | - | - | - | To update | -https://github.com/tidyverse/ggplot2 | -Visualization, Statistics | -ez_histograms | -artbio | -https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms | -https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms | -3.4.4 | -r-ggplot2 | -2.2.1 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | fargene | -fargene | -fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) | -fargene | -fargene | -- | fARGene | -fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. | -Antimicrobial resistance prediction | -Metagenomics, Microbiology, Public health and epidemiology | -Up-to-date | -https://github.com/fannyhb/fargene | -Sequence Analysis | -fargene | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene | -0.1 | -fargene | -0.1 | -Antimicrobial resistance prediction | -Metagenomics, Microbiology, Public health and epidemiology | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -52 | -459 | -False | -
- | fastani | -fastani | -Fast alignment-free computation of whole-genome Average Nucleotide Identity | -fastani | -fastani | -- | FastANI | -FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. | -Genome alignment, Sequence similarity search | -Microbiology, Genetic variation | -To update | -https://github.com/ParBLiSS/FastANI | -Sequence Analysis | -fastani | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani | -1.3 | -fastani | -1.34 | -Genome alignment, Sequence similarity search | -Microbiology, Genetic variation | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -250 | -3498 | -False | -
- | fastk | -fastk_fastk | -FastK: A K-mer counter (for HQ assembly data sets) | -- | - | - | - | - | - | - | To update | -https://github.com/thegenemyers/FASTK | -Assembly | -fastk | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk | -1.0.0 | -fastk | -1.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | fastp | -fastp | -Fast all-in-one preprocessing for FASTQ files | -fastp | -fastp | -- | fastp | -A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. | -Sequencing quality control, Sequence contamination filtering | -Sequence analysis, Probes and primers | -Up-to-date | -https://github.com/OpenGene/fastp | -Sequence Analysis | -fastp | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp | -0.23.4 | -fastp | -0.23.4 | -Sequence contamination filtering | -Probes and primers | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -2803 | -1055760 | -False | -
- | fastqe | -fastqe | -FASTQE | -fastqe | -fastqe | -- | FASTQE | -Compute quality stats for FASTQ files and print those stats as emoji... for some reason. | -Sequencing quality control | -Sequence analysis, Sequencing | -To update | -https://fastqe.com/ | -Sequence Analysis | -fastqe | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe | -0.3.1+galaxy0 | -fastqe | -0.3.1 | -Sequencing quality control | -Sequence analysis, Sequencing | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1266 | -4333 | -False | -
- | fasttree | -fasttree | -FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL | -fasttree | -fasttree | -- | FastTree | -Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. | -Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) | -Phylogenetics, Sequence analysis | -To update | -http://www.microbesonline.org/fasttree/ | -Phylogenetics | -fasttree | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree | -2.1.10 | -fasttree | -2.1.11 | -- | Phylogenetics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -379 | -55434 | -False | -
- | featurecounts | -featurecounts | -featureCounts counts the number of reads aligned to defined masked regions in a reference genome | -featurecounts | -featurecounts | -- | FeatureCounts | -featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. | -Read summarisation, RNA-Seq quantification | -RNA-Seq | -To update | -http://bioinf.wehi.edu.au/featureCounts | -RNA, Transcriptomics, Sequence Analysis | -featurecounts | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts | -2.0.3 | -subread | -2.0.6 | -Read summarisation, RNA-Seq quantification | -RNA-Seq | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -1 | -4679 | -696399 | -False | -
- | filter_spades_repeats | -filter_spades_repeat | -Remove short and repeat contigs/scaffolds | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/galaxy_tools/ | -Assembly | -filter_spades_repeats | -nml | -https://github.com/phac-nml/galaxy_tools/ | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats | -1.0.1 | -perl-bioperl | -1.7.8 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | filtlong | -filtlong | -Filtlong - Filtering long reads by quality | -filtlong | -filtlong | -- | Filtlong | -Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. | -Filtering, Sequencing quality control | -- | Up-to-date | -https://github.com/rrwick/Filtlong | -Fastq Manipulation, Sequence Analysis | -filtlong | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong | -0.2.1 | -filtlong | -0.2.1 | -Filtering, Sequencing quality control | -- | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -617 | -30483 | -False | -
- | flashlfq | -flashlfq | -FlashLFQ mass-spectrometry proteomics label-free quantification | -flashlfq | -flashlfq | -- | FlashLFQ | -FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. | -Label-free quantification | -Proteomics experiment, Proteomics | -To update | -https://github.com/smith-chem-wisc/FlashLFQ | -Proteomics | -flashlfq | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq | -1.0.3.1 | -flashlfq | -1.2.6 | -Label-free quantification | -Proteomics experiment, Proteomics | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -17 | -645 | -False | -
- | flye | -flye | -Assembly of long and error-prone reads. | -Flye | -Flye | -- | Flye | -Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. | -Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly | -Sequence assembly, Metagenomics, Whole genome sequencing, Genomics | -To update | -https://github.com/fenderglass/Flye/ | -Assembly | -flye | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/flye | -https://github.com/bgruening/galaxytools/tree/master/tools/flye | -2.9.3 | -flye | -2.9.4 | -Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly | -Sequence assembly, Metagenomics, Whole genome sequencing | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1499 | -20904 | -False | -
- | format_metaphlan2_output | -format_metaphlan2_output | -Format MetaPhlAn2 output to extract abundance at different taxonomic levels | -format_metaphlan2_output | -format_metaphlan2_output | -- | Format metaphlan2 output | -This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). | -Formatting | -Taxonomy, Metagenomics | -To update | -- | Metagenomics | -format_metaphlan2_output | -bebatut | -https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ | -https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output | -0.2.0 | -- | - | Formatting | -Taxonomy, Metagenomics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -166 | -5588 | -False | -
- | fraggenescan | -fraggenescan | -Tool for finding (fragmented) genes in short read | -fraggenescan | -fraggenescan | -- | FragGeneScan | -Application for finding (fragmented) genes in short reads | -Gene prediction | -Genetics, Sequence analysis | -To update | -https://sourceforge.net/projects/fraggenescan/ | -Sequence Analysis | -fraggenescan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan | -- | fraggenescan | -1.31 | -Gene prediction | -Genetics, Sequence analysis | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -68 | -1102 | -False | -
- | freyja | -freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants | -lineage abundances estimation | -freyja | -freyja | -- | - | - | - | - | To update | -https://github.com/andersen-lab/Freyja | -Metagenomics, Sequence Analysis | -freyja | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja | -1.4.4 | -freyja | -1.5.1 | -- | - | 2 | -0 | -4 | -0 | -2 | -0 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -55 | -20021 | -False | -
- | frogs | -FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom | -Suite for metabarcoding analysis | -frogs | -frogs | -- | FROGS | -The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. | -Taxonomic classification | -Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing | -To update | -http://frogs.toulouse.inrae.fr/ | -Metagenomics | -frogs | -frogs | -https://github.com/geraldinepascal/FROGS-wrappers/ | -https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs | -4.1.0 | -frogs | -5.0.0 | -Taxonomic classification | -Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing | -0 | -0 | -0 | -28 | -0 | -0 | -0 | -28 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -18 | -18 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | funannotate | -funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort | -Funannotate is a genome prediction, annotation, and comparison software package. | -funannotate | -funannotate | -- | funannotate | -funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). | -Genome annotation | -Genomics | -To update | -https://funannotate.readthedocs.io | -Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate | -1.8.15 | -- | - | Genome annotation | -Genomics | -3 | -5 | -5 | -5 | -3 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -900 | -5906 | -False | -
- | getmlst | -getmlst | -Download MLST datasets by species from pubmlst.org | -- | - | - | - | - | - | - | To update | -- | Sequence Analysis | -getmlst | -nml | -- | https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst | -0.1.4.1 | -srst2 | -0.2.0 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | ggplot2 | -ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin | -ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. | -ggplot2 | -ggplot2 | -- | ggplot2 | -Plotting system for R, based on the grammar of graphics. | -Visualisation | -Data visualisation | -To update | -https://github.com/tidyverse/ggplot2 | -Visualization | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 | -3.4.0 | -r-base | -- | Visualisation | -Data visualisation | -5 | -5 | -5 | -5 | -5 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -1388 | -22148 | -False | -
- | gi2taxonomy | -Fetch Taxonomic Ranks | -Fetch taxonomic representation | -gi2taxonomy | -gi2taxonomy | -- | gi2taxonomy | -The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). | -Database search, ID mapping | -Taxonomy | -To update | -https://bitbucket.org/natefoo/taxonomy | -Metagenomics | -gi2taxonomy | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy | -https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy | -1.1.1 | -taxonomy | -0.10.0 | -Database search, ID mapping | -Taxonomy | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -27 | -660 | -False | -
- | glimmer | -glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based | -Glimmer makes gene predictions. | -gemini | -gemini | -- | GEMINI | -GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. | -Sequence analysis, Genetic variation analysis | -Sequence analysis | -To update | -https://ccb.jhu.edu/software/glimmer/ | -Sequence Analysis | -- | bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer | -- | glimmer | -3.02 | -Sequence analysis, Genetic variation analysis | -Sequence analysis | -0 | -0 | -4 | -0 | -0 | -0 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -187 | -3965 | -False | -
- | glimmer_hmm | -- | GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) | -- | - | - | - | - | - | - | To update | -https://ccb.jhu.edu/software/glimmerhmm/ | -Sequence Analysis | -glimmer_hmm | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm | -https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm | -- | - | - | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | goenrichment | -goenrichment, goslimmer | -Performs GO Enrichment analysis. | -goenrichment | -goenrichment | -- | GOEnrichment | -GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de CiĂŞncia. | -Gene-set enrichment analysis | -Transcriptomics | -Up-to-date | -https://github.com/DanFaria/GOEnrichment | -Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment | -2.0.1 | -goenrichment | -2.0.1 | -Gene-set enrichment analysis | -Transcriptomics | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -408 | -5484 | -False | -
- | goseq | -goseq | -goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data | -goseq | -goseq | -- | GOseq | -Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. | -Gene functional annotation | -RNA-Seq | -To update | -https://bioconductor.org/packages/release/bioc/html/goseq.html | -Statistics, RNA, Micro-array Analysis | -goseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq | -1.50.0 | -bioconductor-goseq | -1.54.0 | -Gene functional annotation | -RNA-Seq | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1210 | -19167 | -False | -
- | graphlan | -graphlan, graphlan_annotate | -GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees | -graphlan | -graphlan | -- | GraPhlAn | -GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. | -Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification | -Metagenomics, Phylogenetics, Phylogenomics, Cladistics | -To update | -https://github.com/biobakery/graphlan | -Metagenomics, Graphics, Phylogenetics | -graphlan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan | -- | graphlan | -1.1.3 | -Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification | -Metagenomics, Phylogenetics, Phylogenomics, Cladistics | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -432 | -9277 | -False | -
- | graphmap | -graphmap_align, graphmap_overlap | -Mapper for long, error-prone reads. | -graphmap | -graphmap | -- | graphmap | -Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 | -Sequence trimming, EST assembly, Read mapping | -Gene transcripts, RNA-Seq, RNA splicing | -To update | -https://github.com/isovic/graphmap/ | -Assembly | -graphmap | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/graphmap | -https://github.com/bgruening/galaxytools/tree/master/tools/graphmap | -0.5.2 | -graphmap | -0.6.3 | -Sequence trimming, EST assembly, Read mapping | -Gene transcripts, RNA-Seq, RNA splicing | -0 | -0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -136 | -6651 | -False | -
- | gtdbtk | -gtdbtk_classify_wf | -GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. | -GTDB-Tk | -GTDB-Tk | -- | GTDB-Tk | -a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). | -Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval | -Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins | -To update | -https://github.com/Ecogenomics/GTDBTk | -Metagenomics | -gtdbtk | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk | -2.3.2 | -gtdbtk | -2.4.0 | -Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval | -Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | gubbins | -gubbins | -Gubbins - bacterial recombination detection | -gubbins | -gubbins | -- | Gubbins | -Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. | -Genotyping, Phylogenetic inference, Ancestral reconstruction | -Phylogeny, Genotype and phenotype, Whole genome sequencing | -To update | -- | Sequence Analysis | -gubbins | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins | -3.2.1 | -gubbins | -3.3.5 | -Genotyping, Phylogenetic inference, Ancestral reconstruction | -Phylogeny, Genotype and phenotype, Whole genome sequencing | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -145 | -3340 | -False | -
- | hamronization | -hamronize_summarize, hamronize_tool | -Convert AMR gene detection tool output to hAMRonization specification format. | -hamronization | -hamronization | -- | hAMRonization | -Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure | -Data handling, Antimicrobial resistance prediction, Parsing | -Public health and epidemiology, Microbiology, Bioinformatics | -Up-to-date | -https://github.com/pha4ge/hAMRonization | -Sequence Analysis | -hamronization | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization | -1.1.4 | -hamronization | -1.1.4 | -Antimicrobial resistance prediction, Parsing | -Public health and epidemiology, Microbiology, Bioinformatics | -0 | -0 | -2 | -2 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -117 | -4459 | -False | -
- | hansel | -bio_hansel | -Heidelberg and Enteritidis SNP Elucidation | -Biohansel | -Biohansel | -- | BioHansel | -BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. | -Genotyping, SNP detection, Genome assembly | -Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science | -Up-to-date | -https://github.com/phac-nml/bio_hansel | -Sequence Analysis | -bio_hansel | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel | -2.6.1 | -bio_hansel | -2.6.1 | -Genotyping, SNP detection, Genome assembly | -Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -18 | -339 | -False | -
- | hifiasm_meta | -hifiasm_meta | -A hifiasm fork for metagenome assembly using Hifi reads. | -hifiasm-meta | -hifiasm-meta | -- | Hifiasm-meta | -Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. | -Sequence assembly | -Sequence assembly, Metagenomics | -To update | -https://github.com/xfengnefx/hifiasm-meta | -Metagenomics | -hifiasm_meta | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta | -0.3.1 | -hifiasm_meta | -hamtv0.3.1 | -Sequence assembly | -Sequence assembly, Metagenomics | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -12 | -137 | -False | -
- | hivtrace | -hivtrace | -An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. | -- | - | - | - | - | - | - | To update | -- | Sequence Analysis | -hivtrace | -nml | -https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace | -1.0.1 | -hivtrace | -1.5.0 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | hmmer3 | -hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer | -HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). | -hmmer3 | -hmmer3 | -- | HMMER3 | -This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. | -Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search | -Sequence analysis, Sequence sites, features and motifs, Gene and protein families | -Up-to-date | -http://hmmer.org/ | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 | -3.4 | -hmmer | -3.4 | -Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search | -Sequence analysis, Sequence sites, features and motifs, Gene and protein families | -0 | -12 | -12 | -12 | -0 | -12 | -12 | -12 | -0 | -0 | -0 | -0 | -0 | -0 | -12 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -12 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -12 | -12 | -439 | -33702 | -False | -
- | humann | -humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways | -HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution | -humann | -humann | -- | humann | -HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” | -Species frequency estimation, Taxonomic classification, Phylogenetic analysis | -Metagenomics, Phylogenomics | -To update | -http://huttenhower.sph.harvard.edu/humann | -Metagenomics | -humann | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann | -3.8 | -humann | -3.9 | -Species frequency estimation, Taxonomic classification, Phylogenetic analysis | -Metagenomics, Phylogenomics | -6 | -12 | -13 | -13 | -6 | -12 | -13 | -13 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -13 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -13 | -13 | -1045 | -19521 | -False | -
- | hyphy | -hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary | -Hypothesis Testing using Phylogenies | -HyPhy | -HyPhy | -- | HyPhy | -Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. | -Statistical calculation | -Phylogeny, Small molecules, Molecular interactions, pathways and networks | -To update | -http://www.hyphy.org | -Phylogenetics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy | -2.5.47 | -hyphy | -2.5.62 | -Statistical calculation | -Phylogeny, Small molecules, Molecular interactions, pathways and networks | -17 | -2 | -17 | -2 | -17 | -2 | -17 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -17 | -12 | -161 | -10370 | -False | -
- | hypo | -hypo | -Super Fast & Accurate Polisher for Long Read Genome Assemblies | -HyPo | -HyPo | -- | HyPo | -HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. | -Optimisation and refinement, Genome assembly | -Sequence assembly, Genomics | -Up-to-date | -https://github.com/kensung-lab/hypo | -Assembly | -hypo | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo | -1.0.3 | -hypo | -1.0.3 | -Optimisation and refinement, Genome assembly | -Sequence assembly, Genomics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -39 | -354 | -False | -
- | icescreen | -icescreen | -ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. | -icescreen | -icescreen | -- | ICEscreen | -A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. | -Database search, Protein feature detection | -Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation | -To update | -https://icescreen.migale.inrae.fr/ | -Genome annotation | -icescreen | -iuc | -https://forgemia.inra.fr/ices_imes_analysis/icescreen | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen | -1.3.1 | -icescreen | -1.3.2 | -Database search, Protein feature detection | -Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | idba_ud | -idba_hybrid, idba_tran, idba_ud | -Wrappers for the idba assembler variants. | -idba | -idba | -- | IDBA | -A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. | -Sequence assembly | -Sequence assembly | -To update | -https://i.cs.hku.hk/~alse/hkubrg/projects/index.html | -Assembly | -idba | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud | -- | idba | -1.1.3 | -Sequence assembly | -Sequence assembly | -3 | -0 | -3 | -3 | -3 | -0 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -69 | -1127 | -False | -
- | infernal | -infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat | -Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. | -infernal | -infernal | -- | Infernal | -Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. | -Nucleic acid feature detection | -Sequence sites, features and motifs, Structural genomics | -To update | -http://infernal.janelia.org/ | -RNA | -infernal | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/infernal | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal | -1.1.4 | -infernal | -1.1.5 | -Nucleic acid feature detection | -Sequence sites, features and motifs, Structural genomics | -0 | -6 | -6 | -0 | -0 | -6 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -6 | -67 | -100294 | -False | -
- | instrain | -instrain_compare, instrain_profile | -InStrain is a tool for analysis of co-occurring genome populations from metagenomes | -instrain | -instrain | -- | InStrain | -InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification | -SNP detection, Genome comparison | -Mapping, Metagenomics | -To update | -https://instrain.readthedocs.io/en/latest/# | -Metagenomics | -instrain | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain | -1.5.3 | -instrain | -1.9.0 | -SNP detection, Genome comparison | -Mapping, Metagenomics | -0 | -0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -5 | -94 | -False | -
- | integron_finder | -integron_finder | -"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching" | -integron_finder | -integron_finder | -- | Integron Finder | -A tool to detect Integron in DNA sequences. | -Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation | -Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis | -Up-to-date | -https://github.com/gem-pasteur/Integron_Finder | -Sequence Analysis | -integronfinder | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder | -2.0.5 | -integron_finder | -2.0.5 | -Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation | -Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -58 | -52965 | -False | -
- | interproscan | -interproscan | -Interproscan queries the interpro database and provides annotations. | -interproscan_ebi | -interproscan_ebi | -- | InterProScan (EBI) | -Scan sequences against the InterPro protein signature databases. | -Sequence motif recognition, Protein feature detection | -Gene and protein families, Sequence analysis | -To update | -http://www.ebi.ac.uk/Tools/pfa/iprscan5/ | -Sequence Analysis | -interproscan | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan | -5.59-91.0 | -interproscan | -5.59_91.0 | -Sequence motif recognition, Protein feature detection | -Gene and protein families, Sequence analysis | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -677 | -35243 | -False | -
- | iprscan5 | -- | Interproscan queries the interpro database and provides annotations. | -- | - | - | - | - | - | - | To update | -http://www.ebi.ac.uk/Tools/pfa/iprscan5/ | -Sequence Analysis | -iprscan5 | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 | -https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 | -- | - | - | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | iqtree | -iqtree | -Efficient phylogenomic software by maximum likelihood | -iqtree | -iqtree | -- | iqtree | -A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time | -Phylogenetic analysis, Sequence analysis | -Phylogenetics | -Up-to-date | -http://www.iqtree.org/ | -Phylogenetics | -iqtree | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree | -2.3.4 | -iqtree | -2.3.4 | -Phylogenetic analysis, Sequence analysis | -Phylogenetics | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -681 | -21598 | -False | -
- | isescan | -isescan | -"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements." | -ISEScan | -ISEScan | -- | ISEScan | -Automated identification of insertion sequence elements in prokaryotic genomes. | -Structural variation detection | -Genomics, DNA structural variation, Sequence analysis, Genetic variation | -To update | -https://github.com/xiezhq/ISEScan | -Sequence Analysis | -ISEScan | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan | -1.7.2.3 | -isescan | -1.7.2.1 | -Structural variation detection | -Genomics, Sequence analysis, Genetic variation | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -50 | -57581 | -False | -
- | itsx | -itsx | -ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. | -ITSx | -ITSx | -- | ITSx | -TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. | -Sequence feature detection | -Functional, regulatory and non-coding RNA, Microbiology | -Up-to-date | -https://microbiology.se/software/itsx/ | -Metagenomics | -itsx | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/itsx | -https://github.com/bgruening/galaxytools/tree/master/tools/itsx | -1.1.3 | -itsx | -1.1.3 | -Sequence feature detection | -Functional, regulatory and non-coding RNA, Microbiology | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -38 | -868 | -False | -
- | ivar | -ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants | -iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/andersen-lab/ivar | -Sequence Analysis | -ivar | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar | -1.4.3 | -ivar | -1.4.3 | -- | - | 5 | -5 | -5 | -5 | -5 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -0 | -4 | -0 | -0 | -0 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -1171 | -1224275 | -False | -
- | jbrowse | -jbrowse_to_standalone, jbrowse | -JBrowse Genome Browser integrated as a Galaxy Tool | -jbrowse | -jbrowse | -- | JBrowse | -Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. | -Genome visualisation | -Genomics | -Up-to-date | -https://jbrowse.org | -Sequence Analysis | -jbrowse | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse | -1.16.11 | -jbrowse | -1.16.11 | -Genome visualisation | -Genomics | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -2346 | -18229 | -False | -
- | jellyfish | -jellyfish | -Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA | -Jellyfish | -Jellyfish | -- | Jellyfish | -A command-line algorithm for counting k-mers in DNA sequence. | -k-mer counting | -Sequence analysis, Genomics | -To update | -https://github.com/gmarcais/Jellyfish | -Assembly | -jellyfish | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish | -- | kmer-jellyfish | -2.3.1 | -k-mer counting | -Sequence analysis, Genomics | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -91 | -1138 | -False | -
- | kat_filter | -kat_@EXECUTABLE@ | -Filtering kmers or reads from a database of kmers hashes | -- | - | - | - | - | - | - | To update | -- | Sequence Analysis | -kat_filter | -nml | -- | https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter | -2.3 | -kat | -2.4.2 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | kc-align | -kc-align | -Kc-Align custom tool | -kc-align | -kc-align | -- | kc-align | -A fast and accurate tool for performing codon-aware multiple sequence alignments | -Multiple sequence alignment | -Mapping | -Up-to-date | -https://github.com/davebx/kc-align | -Sequence Analysis | -kc_align | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align | -1.0.2 | -kcalign | -1.0.2 | -Multiple sequence alignment | -Mapping | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -19 | -363 | -False | -
- | khmer | -khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median | -In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more | -khmer | -khmer | -- | khmer | -khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. | -Standardisation and normalisation, De-novo assembly | -Sequence assembly | -Up-to-date | -https://khmer.readthedocs.org/ | -Assembly, Next Gen Mappers | -khmer | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer | -3.0.0a3 | -khmer | -3.0.0a3 | -Standardisation and normalisation, De-novo assembly | -Sequence assembly | -8 | -8 | -8 | -0 | -8 | -8 | -8 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -8 | -8 | -63 | -2022 | -False | -
- | kleborate | -kleborate | -Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) | -kleborate | -kleborate | -- | Kleborate | -Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). | -Multilocus sequence typing, Genome assembly, Virulence prediction | -Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing | -Up-to-date | -https://github.com/katholt/Kleborate/wiki | -Metagenomics | -kleborate | -iuc | -https://github.com/katholt/Kleborate | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate | -2.3.2 | -kleborate | -2.3.2 | -Multilocus sequence typing, Genome assembly, Virulence prediction | -Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -38 | -319 | -False | -
- | kofamscan | -kofamscan | -Gene function annotation tool based on KEGG Orthology and hidden Markov model | -kofamscan | -kofamscan | -- | kofamscan | -KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. | -Sequence analysis, Gene functional annotation | -Genomics | -Up-to-date | -https://github.com/takaram/kofam_scan | -Sequence Analysis | -kofamscan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan | -1.3.0 | -kofamscan | -1.3.0 | -Sequence analysis, Gene functional annotation | -Genomics | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -33 | -594 | -False | -
- | kraken | -kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken | -Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. | -kraken | -kraken | -- | Kraken | -System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. | -Taxonomic classification | -Taxonomy, Metagenomics | -To update | -http://ccb.jhu.edu/software/kraken/ | -Metagenomics | -kraken | -devteam | -https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken | -- | kraken | -1.1.1 | -Taxonomic classification | -Taxonomy, Metagenomics | -5 | -5 | -5 | -5 | -5 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -5 | -5 | -1209 | -33778 | -False | -
- | kraken2 | -kraken2 | -Kraken2 for taxonomic designation. | -kraken2 | -kraken2 | -- | kraken2 | -Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. | -Taxonomic classification | -Taxonomy, Metagenomics | -Up-to-date | -http://ccb.jhu.edu/software/kraken/ | -Metagenomics | -kraken2 | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 | -2.1.3 | -kraken2 | -2.1.3 | -Taxonomic classification | -Taxonomy, Metagenomics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -1 | -2367 | -185308 | -False | -
- | kraken2tax | -Kraken2Tax | -Convert Kraken output to Galaxy taxonomy data. | -- | - | - | - | - | - | - | To update | -https://bitbucket.org/natefoo/taxonomy | -Metagenomics | -kraken2tax | -devteam | -https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ | -https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax | -1.2+galaxy0 | -gawk | -- | - | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -481 | -14683 | -False | -
- | kraken_biom | -kraken_biom | -Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/smdabdoub/kraken-biom | -Metagenomics | -kraken_biom | -iuc | -https://github.com/smdabdoub/kraken-biom | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom | -1.2.0 | -kraken-biom | -1.2.0 | -- | - | 0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -182 | -1444 | -False | -
- | kraken_taxonomy_report | -kraken_taxonomy_report | -Kraken taxonomy report | -Kraken-Taxonomy-Report | -Kraken-Taxonomy-Report | -- | Kraken-Taxonomy-Report | -view report of classification for multiple samples | -Visualisation, Classification | -Metagenomics, Taxonomy | -To update | -https://github.com/blankenberg/Kraken-Taxonomy-Report | -Metagenomics | -kraken_taxonomy_report | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report | -0.0.3 | -biopython | -1.70 | -Visualisation, Classification | -Metagenomics, Taxonomy | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -354 | -2527 | -False | -
- | krakentools | -krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa | -KrakenTools is a suite of scripts to be used alongside the Kraken | -krakentools | -krakentools | -- | KrakenTools | -KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files | -Visualisation, Aggregation | -Taxonomy, Metagenomics | -Up-to-date | -https://github.com/jenniferlu717/KrakenTools | -Metagenomics | -krakentools | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools | -1.2 | -krakentools | -1.2 | -Visualisation, Aggregation | -Taxonomy, Metagenomics | -1 | -6 | -6 | -6 | -1 | -6 | -6 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -0 | -703 | -16525 | -False | -
- | krocus | -krocus | -Predict MLST directly from uncorrected long reads | -krocus | -krocus | -- | krocus | -Predict MLST directly from uncorrected long reads | -Multilocus sequence typing, k-mer counting | -Public health and epidemiology | -To update | -https://github.com/quadram-institute-bioscience/krocus | -Sequence Analysis | -krocus | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus | -1.0.1 | -krocus | -1.0.3 | -Multilocus sequence typing, k-mer counting | -Public health and epidemiology | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | lca_wrapper | -lca1 | -Find lowest diagnostic rank | -- | - | - | - | - | - | - | To update | -https://bitbucket.org/natefoo/taxonomy | -Metagenomics | -lca_wrapper | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper | -https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper | -1.0.1 | -taxonomy | -0.10.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -2 | -137 | -False | -
- | legsta | -legsta | -Performs in silico Legionella pneumophila sequence based typing. | -legsta | -legsta | -- | legsta | -Performs in silico Legionella pneumophila sequence based typing | -Sequence analysis | -Public health and epidemiology | -Up-to-date | -https://github.com/tseemann/legsta | -Sequence Analysis | -legsta | -iuc | -https://github.com/tseemann/legsta | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta | -0.5.1 | -legsta | -0.5.1 | -Sequence analysis | -Public health and epidemiology | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -7 | -55 | -False | -
- | lighter | -lighter | -Lighter is a kmer-based error correction method for whole genome sequencing data | -lighter | -lighter | -- | Lighter | -Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. | -k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection | -Sequencing, Whole genome sequencing, DNA, Genomics | -To update | -https://github.com/mourisl/Lighter | -Sequence Analysis, Fasta Manipulation | -lighter | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/lighter | -https://github.com/bgruening/galaxytools/tree/master/tools/lighter | -1.0 | -lighter | -1.1.3 | -k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection | -Whole genome sequencing, DNA, Genomics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -9 | -152 | -False | -
- | limma_voom | -limma_voom | -Perform RNA-Seq differential expression analysis using limma voom pipeline | -limma | -limma | -- | limma | -Data analysis, linear models and differential expression for microarray data. | -RNA-Seq analysis | -Molecular biology, Genetics | -Up-to-date | -http://bioconductor.org/packages/release/bioc/html/limma.html | -Transcriptomics, RNA, Statistics | -limma_voom | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom | -3.58.1 | -bioconductor-limma | -3.58.1 | -RNA-Seq analysis | -Molecular biology, Genetics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1012 | -20344 | -False | -
- | lineagespot | -lineagespot | -Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) | -lineagespot | -lineagespot | -- | lineagespot | -Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). | -Variant calling | -Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation | -To update | -https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html | -Metagenomics, Sequence Analysis | -lineagespot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot | -1.6.0 | -r-base | -- | Variant calling | -Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -2 | -37 | -False | -
- | lorikeet | -lorikeet_spoligotype | -Tools for M. tuberculosis DNA fingerprinting (spoligotyping) | -lorikeet | -lorikeet | -- | lorikeet | -Tools for M. tuberculosis DNA fingerprinting (spoligotyping) | -Sequence analysis, Genotyping | -Genotype and phenotype | -Up-to-date | -https://github.com/AbeelLab/lorikeet | -Sequence Analysis | -lorikeet_spoligotype | -iuc | -https://github.com/AbeelLab/lorikeet | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet | -20 | -lorikeet | -20 | -Sequence analysis, Genotyping | -Genotype and phenotype | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -9 | -647 | -False | -
- | lotus2 | -lotus2 | -LotuS2 OTU processing pipeline | -lotus2 | -lotus2 | -- | lotus2 | -LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. | -Sequence feature detection, DNA barcoding | -Metagenomics, Taxonomy, Microbial ecology | -Up-to-date | -http://lotus2.earlham.ac.uk/ | -Metagenomics | -lotus2 | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 | -2.32 | -lotus2 | -2.32 | -Sequence feature detection, DNA barcoding | -Metagenomics, Taxonomy, Microbial ecology | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -114 | -936 | -False | -
- | m6anet | -m6anet | -m6anet to detect m6A RNA modifications from nanopore data | -m6Anet | -m6Anet | -- | m6Anet | -Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. | -Quantification, Imputation, Gene expression profiling | -RNA-Seq, Transcriptomics, RNA, Machine learning | -Up-to-date | -https://m6anet.readthedocs.io/en/latest | -Sequence Analysis | -m6anet | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet | -2.1.0 | -m6anet | -2.1.0 | -Quantification, Imputation, Gene expression profiling | -RNA-Seq, Transcriptomics, RNA, Machine learning | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -False | -
- | maaslin2 | -maaslin2 | -MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. | -maaslin2 | -maaslin2 | -- | MaAsLin2 | -MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. | -Filtering, Statistical calculation, Standardisation and normalisation, Visualisation | -Metagenomics, Statistics and probability | -To update | -http://huttenhower.sph.harvard.edu/maaslin | -Metagenomics | -maaslin2 | -iuc | -https://github.com/biobakery/Maaslin2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 | -0.99.12 | -maaslin2 | -1.16.0 | -Filtering, Standardisation and normalisation, Visualisation | -Metagenomics, Statistics and probability | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -29 | -188 | -False | -
- | mafft | -rbc_mafft_add, rbc_mafft | -Multiple alignment program for amino acid or nucleotide sequences | -MAFFT | -MAFFT | -- | MAFFT | -MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. | -Multiple sequence alignment | -Sequence analysis | -To update | -https://mafft.cbrc.jp/alignment/software/ | -RNA | -mafft | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/mafft | -https://github.com/bgruening/galaxytools/tree/master/tools/mafft | -7.520 | -mafft | -7.525 | -Multiple sequence alignment | -Sequence analysis | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -1 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -2 | -0 | -0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -817 | -143045 | -False | -
- | make_nr | -make_nr | -Make a FASTA file non-redundant | -- | - | - | - | - | - | - | To update | -https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr | -Fasta Manipulation, Sequence Analysis | -make_nr | -peterjc | -https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr | -https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr | -0.0.3 | -biopython | -1.70 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | maker | -maker, maker_map_ids | -MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. | -maker | -maker | -- | MAKER | -Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. | -Genome annotation | -Genomics, DNA, Sequence analysis | -To update | -http://www.yandell-lab.org/software/maker.html | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker | -2.31.11 | -maker | -3.01.03 | -Genome annotation | -Genomics, DNA, Sequence analysis | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -554 | -5591 | -False | -
- | mapseq | -mapseq | -fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. | -mapseq | -mapseq | -- | MAPseq | -Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . | -k-mer counting | -Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs | -To update | -https://github.com/jfmrod/MAPseq | -Metagenomics | -mapseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq | -2.1.1 | -perl | -- | k-mer counting | -Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -2 | -167 | -False | -
- | mash | -mash_screen, mash_sketch | -Fast genome and metagenome distance estimation using MinHash | -mash | -mash | -- | Mash | -Fast genome and metagenome distance estimation using MinHash. | -Sequence distance matrix generation | -Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation | -Up-to-date | -https://github.com/marbl/Mash | -Metagenomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash | -2.3 | -mash | -2.3 | -Sequence distance matrix generation | -Metagenomics, Statistics and probability, Sequence analysis, DNA mutation | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -27 | -9763 | -False | -
- | maxbin2 | -maxbin2 | -clusters metagenomic contigs into bins | -maxbin | -maxbin | -- | MaxBin | -Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. | -Sequence assembly | -Metagenomics, Sequence assembly, Microbiology | -To update | -https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html | -Metagenomics | -maxbin2 | -mbernt | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 | -- | maxbin2 | -2.2.7 | -Sequence assembly | -Metagenomics, Sequence assembly, Microbiology | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -1 | -118 | -2059 | -False | -
- | maxquant | -maxquant, maxquant_mqpar | -wrapper for MaxQuant | -maxquant | -maxquant | -- | MaxQuant | -Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. | -Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting | -Proteomics experiment, Proteomics, Statistics and probability | -Up-to-date | -https://www.maxquant.org/ | -Proteomics | -maxquant | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant | -2.0.3.0 | -maxquant | -2.0.3.0 | -Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering | -Proteomics experiment, Proteomics, Statistics and probability | -2 | -2 | -2 | -0 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -415 | -6078 | -False | -
- | mcl | -mcl | -The Markov Cluster Algorithm, a cluster algorithm for graphs | -mcl | -mcl | -- | MCL | -MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. | -Clustering, Network analysis, Gene regulatory network analysis | -Molecular interactions, pathways and networks | -Up-to-date | -https://micans.org/mcl/man/mcl.html | -Sequence Analysis | -mcl | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/mcl | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl | -22.282 | -mcl | -22.282 | -Clustering, Gene regulatory network analysis | -Molecular interactions, pathways and networks | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -10 | -29 | -False | -
- | medaka | -medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant | -Sequence correction provided by ONT Research | -medaka | -medaka | -- | Medaka | -medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. | -Base-calling, Variant calling, Sequence assembly | -Sequence assembly, Machine learning | -To update | -https://github.com/nanoporetech/medaka | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka | -1.7.2 | -medaka | -1.11.3 | -Base-calling, Variant calling, Sequence assembly | -Sequence assembly, Machine learning | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -768 | -99863 | -False | -
- | megahit | -megahit | -An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. | -megahit | -megahit | -- | MEGAHIT | -Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. | -Genome assembly | -Metagenomics, Sequencing, Ecology, Sequence assembly | -Up-to-date | -https://github.com/voutcn/megahit | -Sequence Analysis, Assembly, Metagenomics | -megahit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit | -1.2.9 | -megahit | -1.2.9 | -Genome assembly | -Metagenomics, Sequencing, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -1 | -548 | -9530 | -False | -
- | megahit_contig2fastg | -megahit_contig2fastg | -A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) | -megahit | -megahit | -- | MEGAHIT | -Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. | -Genome assembly | -Metagenomics, Sequencing, Ecology, Sequence assembly | -To update | -https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp | -Sequence Analysis, Assembly, Metagenomics | -megahit_contig2fastg | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg | -1.1.3 | -megahit | -1.2.9 | -Genome assembly | -Metagenomics, Sequencing, Sequence assembly | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -54 | -475 | -False | -
- | megan | -megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma | -MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). | -megan | -megan | -- | MEGAN | -Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzerÂť) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. | -Sequence analysis, Taxonomic classification | -Sequence analysis | -To update | -https://github.com/husonlab/megan-ce | -Sequence Analysis | -megan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan | -6.21.7 | -megan | -6.25.9 | -Sequence analysis, Taxonomic classification | -Sequence analysis | -0 | -0 | -7 | -0 | -0 | -0 | -7 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -7 | -0 | -261 | -3610 | -False | -
- | meningotype | -meningotype | -Assign sequence type to N. meningitidis genome assemblies | -meningotype | -meningotype | -- | meningotype | -In silico typing of Neisseria meningitidis contigs. | -Genotyping, Multilocus sequence typing | -Microbiology, Genotype and phenotype | -Up-to-date | -https://github.com/MDU-PHL/meningotype | -Sequence Analysis | -meningotype | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype | -0.8.5 | -meningotype | -0.8.5 | -Multilocus sequence typing | -Microbiology, Genotype and phenotype | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | merqury | -merqury, merquryplot | -Merqury is a tool for evaluating genomes assemblies based of k-mer operations. | -merqury | -merqury | -- | Merqury | -Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. | -Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly | -Sequence assembly, Whole genome sequencing, Plant biology | -Up-to-date | -https://github.com/marbl/merqury | -Assembly | -merqury | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury | -1.3 | -merqury | -1.3 | -Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly | -Sequence assembly, Whole genome sequencing, Plant biology | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -244 | -2483 | -False | -
- | meryl | -meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode | -Meryl a k-mer counter. | -meryl | -meryl | -- | Meryl | -Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. | -k-mer counting | -Whole genome sequencing, Genomics, Sequence analysis, Sequencing | -Up-to-date | -https://github.com/marbl/meryl | -Assembly | -meryl | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl | -1.3 | -merqury | -1.3 | -k-mer counting | -Whole genome sequencing, Genomics, Sequence analysis | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | metabat2 | -metabat2_jgi_summarize_bam_contig_depths, metabat2 | -MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. | -MetaBAT_2 | -MetaBAT_2 | -- | MetaBAT 2 | -an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning | -Read binning, Sequence assembly, Genome annotation | -Metagenomics, Sequence assembly, Metagenomic sequencing | -To update | -https://bitbucket.org/berkeleylab/metabat/src/master/ | -Metagenomics | -metabat2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 | -2.15 | -metabat2 | -2.17 | -Read binning, Sequence assembly, Genome annotation | -Metagenomics, Sequence assembly, Metagenomic sequencing | -2 | -1 | -2 | -2 | -2 | -1 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -2 | -0 | -192 | -4329 | -False | -
- | metaeuk | -metaeuk_easy_predict | -MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. | -MetaEuk | -MetaEuk | -- | MetaEuk | -MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics | -Homology-based gene prediction | -Metagenomics, Gene and protein families | -To update | -https://github.com/soedinglab/metaeuk | -Sequence Analysis, Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk | -5.34c21f2 | -metaeuk | -6.a5d39d9 | -Homology-based gene prediction | -Metagenomics, Gene and protein families | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -16 | -184 | -False | -
- | metagene_annotator | -metagene_annotator | -MetaGeneAnnotator gene-finding program for prokaryote and phage | -metageneannotator | -metageneannotator | -- | MetaGeneAnnotator | -Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. | -Sequence annotation | -Genomics, Model organisms, Data submission, annotation and curation | -Up-to-date | -http://metagene.nig.ac.jp/ | -Sequence Analysis | -metagene_annotator | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator | -1.0 | -metagene_annotator | -1.0 | -Sequence annotation | -Genomics, Model organisms, Data submission, annotation and curation | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -115 | -636 | -False | -
- | metagenomeseq | -metagenomeseq_normalizaton | -metagenomeSeq Normalization | -metagenomeseq | -metagenomeseq | -- | metagenomeSeq | -Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. | -Sequence visualisation, Statistical calculation | -Metagenomics, Sequencing | -To update | -- | Metagenomics | -metagenomeseq_normalization | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq | -1.16.0-0.0.1 | -bioconductor-metagenomeseq | -1.43.0 | -Sequence visualisation, Statistical calculation | -Metagenomics, Sequencing | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -6 | -753 | -False | -
- | metanovo | -metanovo | -Produce targeted databases for mass spectrometry analysis. | -metanovo | -metanovo | -- | MetaNovo | -An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. | -Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis | -Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules | -Up-to-date | -https://github.com/uct-cbio/proteomics-pipelines | -Proteomics | -metanovo | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo | -1.9.4 | -metanovo | -1.9.4 | -Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis | -Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -15 | -4181 | -False | -
- | metaphlan | -customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan | -MetaPhlAn for Metagenomic Phylogenetic Analysis | -metaphlan | -metaphlan | -- | MetaPhlAn | -Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. | -Nucleic acid sequence analysis, Phylogenetic tree analysis | -Metagenomics, Phylogenomics | -To update | -https://github.com/biobakery/MetaPhlAn | -Metagenomics | -metaphlan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan | -4.0.6 | -metaphlan | -4.1.1 | -Nucleic acid sequence analysis | -Metagenomics, Phylogenomics | -1 | -2 | -4 | -4 | -1 | -2 | -4 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -4 | -499 | -11069 | -False | -
- | metaquantome | -metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz | -quantitative analysis of microbiome taxonomy and function | -metaQuantome | -metaQuantome | -- | metaQuantome | -metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. | -Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference | -Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics | -Up-to-date | -https://github.com/galaxyproteomics/metaquantome/ | -Proteomics | -metaquantome | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome | -2.0.2 | -metaquantome | -2.0.2 | -Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference | -Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics | -0 | -6 | -6 | -0 | -0 | -6 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -6 | -104 | -2522 | -False | -
- | metawrapmg | -metawrapmg_binning | -A flexible pipeline for genome-resolved metagenomic data analysis | -metawrap | -metawrap | -- | MetaWRAP | -MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. | -Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing | -Whole genome sequencing, Metagenomic sequencing, Metagenomics | -Up-to-date | -https://github.com/bxlab/metaWRAP | -Metagenomics | -metawrapmg_binning | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg | -1.3.0 | -metawrap-mg | -1.3.0 | -Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing | -Whole genome sequencing, Metagenomic sequencing, Metagenomics | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | minia | -minia | -Short-read assembler based on a de Bruijn graph | -minia | -minia | -- | Minia | -Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | -Genome assembly | -Sequence assembly | -Up-to-date | -https://gatb.inria.fr/software/minia/ | -Assembly | -minia | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia | -3.2.6 | -minia | -3.2.6 | -Genome assembly | -Sequence assembly | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -109 | -2206 | -False | -
- | miniasm | -miniasm | -Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) | -miniasm | -miniasm | -- | miniasm | -Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. | -De-novo assembly | -Genomics, Sequence assembly | -To update | -https://github.com/lh3/miniasm | -Assembly | -miniasm | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm | -0.3_r179 | -miniasm | -0.3 | -De-novo assembly | -Genomics, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -178 | -11938 | -False | -
- | minipolish | -minipolish | -Polishing miniasm assemblies | -minipolish | -minipolish | -- | minipolish | -A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. | -Localised reassembly, Read depth analysis | -Sequence assembly, Sequencing | -Up-to-date | -https://github.com/rrwick/Minipolish | -Sequence Analysis | -minipolish | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/minipolish | -https://github.com/bgruening/galaxytools/tree/master/tools/minipolish | -0.1.3 | -minipolish | -0.1.3 | -Localised reassembly, Read depth analysis | -Sequence assembly, Sequencing | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -21 | -185 | -False | -
- | miniprot | -miniprot, miniprot_index | -Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. | -miniprot | -miniprot | -- | miniprot | -Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. | -Sequence alignment, Protein sequence analysis | -Sequence sites, features and motifs, Sequence analysis | -Up-to-date | -https://github.com/lh3/miniprot | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot | -0.13 | -miniprot | -0.13 | -Sequence alignment, Protein sequence analysis | -Sequence sites, features and motifs, Sequence analysis | -2 | -0 | -2 | -2 | -2 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -30 | -842 | -False | -
- | mitos | -mitos, mitos2 | -de-novo annotation of metazoan mitochondrial genomes | -mitos | -mitos | -- | MITOS | -De novo metazoan mitochondrial genome annotation. | -Genome annotation | -Zoology, Whole genome sequencing | -To update | -http://mitos.bioinf.uni-leipzig.de/ | -Sequence Analysis | -mitos | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos | -1.1.7 | -mitos | -2.1.9 | -Genome annotation | -Zoology, Whole genome sequencing | -1 | -1 | -2 | -0 | -1 | -1 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -1 | -236 | -100920 | -False | -
- | mlst | -mlst, mlst_list | -Scan contig files against PubMLST typing schemes | -mlst | -mlst | -- | MLST | -Multi Locus Sequence Typing from an assembled genome or from a set of reads. | -Multilocus sequence typing | -Immunoproteins and antigens | -To update | -https://github.com/tseemann/mlst | -Sequence Analysis | -mlst | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst | -2.22.0 | -mlst | -2.23.0 | -Multilocus sequence typing | -Immunoproteins and antigens | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -635 | -9304 | -False | -
- | mob_suite | -mob_recon, mob_typer | -MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/mob-suite | -Sequence Analysis | -mob_suite | -nml | -https://github.com/phac-nml/mob-suite | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite | -3.0.3 | -mob_suite | -3.1.9 | -- | - | 0 | -2 | -2 | -2 | -0 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -322 | -89021 | -False | -
- | mothur | -mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn | -Mothur wrappers | -mothur | -mothur | -- | mothur | -Open-source, platform-independent, community-supported software for describing and comparing microbial communities | -DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis | -Microbial ecology, Taxonomy, Sequence analysis, Phylogeny | -To update | -https://www.mothur.org | -Metagenomics | -mothur | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur | -1.0 | -mothur | -1.48.0 | -DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis | -Microbial ecology, Taxonomy, Sequence analysis, Phylogeny | -129 | -129 | -129 | -129 | -129 | -129 | -129 | -129 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -128 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -129 | -129 | -14353 | -302916 | -False | -
- | mrbayes | -mrbayes | -A program for the Bayesian estimation of phylogeny. | -- | - | - | - | - | - | - | To update | -- | Sequence Analysis | -mrbayes | -nml | -- | https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes | -1.0.2 | -mrbayes | -3.2.7 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | msconvert | -msconvert | -msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container | -msconvert | -msconvert | -- | msConvert | -msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. | -Filtering, Formatting | -Proteomics, Proteomics experiment | -To update | -http://proteowizard.sourceforge.net/tools.shtml | -Proteomics | -msconvert | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert | -3.0.20287 | -- | - | Filtering, Formatting | -Proteomics, Proteomics experiment | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -189 | -19958 | -False | -
- | msstatstmt | -msstatstmt | -MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling | -- | - | - | - | - | - | - | To update | -http://msstats.org/msstatstmt/ | -Proteomics | -msstatstmt | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt | -2.0.0 | -bioconductor-msstatstmt | -2.10.0 | -- | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -71 | -726 | -False | -
- | multigsea | -multigsea | -GSEA-based pathway enrichment analysis for multi-omics data | -multiGSEA | -multiGSEA | -- | multiGSEA | -A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. | -Gene-set enrichment analysis, Aggregation, Pathway analysis | -Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules | -Up-to-date | -https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html | -Transcriptomics, Proteomics, Statistics | -multigsea | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea | -1.12.0 | -bioconductor-multigsea | -1.12.0 | -Gene-set enrichment analysis, Aggregation, Pathway analysis | -Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -2 | -53 | -False | -
- | multiqc | -multiqc | -MultiQC aggregates results from bioinformatics analyses across many samples into a single report | -multiqc | -multiqc | -- | MultiQC | -MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. | -Validation, Sequencing quality control | -Sequencing, Bioinformatics, Sequence analysis, Genomics | -To update | -http://multiqc.info/ | -Fastq Manipulation, Statistics, Visualization | -multiqc | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc | -1.11 | -multiqc | -1.22.3 | -Sequencing quality control | -Sequencing, Bioinformatics, Sequence analysis, Genomics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -1 | -8320 | -162790 | -False | -
- | mykrobe | -mykrobe_predict | -Antibiotic resistance predictions | -Mykrobe | -Mykrobe | -- | Mykrobe | -Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed | -Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming | -Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics | -To update | -https://github.com/Mykrobe-tools/mykrobe | -Sequence Analysis | -mykrobe | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe | -0.10.0 | -mykrobe | -0.13.0 | -Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming | -Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | mykrobe_parser | -mykrobe_parseR | -RScript to parse the results of mykrobe predictor. | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/mykrobe-parser | -Sequence Analysis | -mykrobe_parser | -nml | -https://github.com/phac-nml/mykrobe-parser | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser | -0.1.4.1 | -r-base | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | mz_to_sqlite | -mz_to_sqlite | -Creates a SQLite database for proteomics data | -mztosqlite | -mztosqlite | -- | mzToSQLite | -Convert proteomics data files into a SQLite database | -Conversion, Peptide database search | -Proteomics, Biological databases | -To update | -https://github.com/galaxyproteomics/mzToSQLite | -Proteomics | -mz_to_sqlite | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite | -2.1.1+galaxy0 | -mztosqlite | -2.1.1 | -Conversion, Peptide database search | -Proteomics, Biological databases | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -33 | -844 | -False | -
- | nanocompore | -nanocompore_db, nanocompore_sampcomp | -Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. | -Nanocompore | -Nanocompore | -- | Nanocompore | -RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro | -Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting | -Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites | -To update | -https://nanocompore.rna.rocks/ | -Sequence Analysis | -nanocompore | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore | -1.0.0rc3.post2 | -nanocompore | -1.0.4 | -PolyA signal detection, Genotyping, k-mer counting | -Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites | -0 | -1 | -2 | -0 | -0 | -1 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -3 | -836 | -False | -
- | nanoplot | -nanoplot | -Plotting tool for long read sequencing data and alignments | -nanoplot | -nanoplot | -- | NanoPlot | -NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences | -Scatter plot plotting, Box-Whisker plot plotting | -Genomics | -Up-to-date | -https://github.com/wdecoster/NanoPlot | -Visualization | -nanoplot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot | -1.42.0 | -nanoplot | -1.42.0 | -Scatter plot plotting, Box-Whisker plot plotting | -Genomics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -2195 | -63235 | -False | -
- | nanopolishcomp | -nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate | -NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. | -nanopolishcomp | -nanopolishcomp | -- | NanopolishComp | -NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. | -Methylation analysis, Collapsing methods | -Sequence analysis, Sequencing, Genetic variation | -To update | -https://a-slide.github.io/NanopolishComp | -Sequence Analysis | -nanopolishcomp | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp | -0.6.11 | -nanopolishcomp | -0.6.12 | -Methylation analysis, Collapsing methods | -Sequence analysis, Sequencing, Genetic variation | -0 | -0 | -2 | -2 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -15 | -1074 | -False | -
- | ncbi_blast_plus | -blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper | -NCBI BLAST+ | -- | - | - | - | - | - | - | To update | -https://blast.ncbi.nlm.nih.gov/ | -Sequence Analysis | -ncbi_blast_plus | -devteam | -https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus | -https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus | -2.14.1 | -python | -- | - | - | 16 | -16 | -16 | -16 | -16 | -16 | -16 | -16 | -6 | -0 | -0 | -15 | -0 | -0 | -15 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -16 | -15 | -16 | -0 | -0 | -0 | -0 | -0 | -0 | -16 | -0 | -0 | -0 | -0 | -16 | -0 | -0 | -0 | -16 | -15 | -4066 | -365597 | -False | -
- | ncbi_fcs_gx | -ncbi_fcs_gx | -FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). | -ncbi_fcs | -ncbi_fcs | -- | NCBI fcs | -The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. | -Sequence assembly validation, Sequence trimming, Sequence contamination filtering | -Sequence analysis, Sequence assembly | -Up-to-date | -https://github.com/ncbi/fcs-gx | -Sequence Analysis | -ncbi_fcs_gx | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx | -0.5.0 | -ncbi-fcs-gx | -0.5.0 | -Sequence assembly validation, Sequence trimming, Sequence contamination filtering | -Sequence analysis, Sequence assembly | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | newick_utils | -newick_display | -Perform operations on Newick trees | -newick_utilities | -newick_utilities | -- | Newick Utilities | -The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. | -Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction | -Phylogeny, Genomics, Computer science | -To update | -http://cegg.unige.ch/newick_utils | -Visualization, Metagenomics | -newick_utils | -iuc | -https://github.com/tjunier/newick_utils | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils | -1.6+galaxy1 | -newick_utils | -1.6 | -- | Phylogeny, Genomics, Computer science | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -448 | -25505 | -False | -
- | nextclade | -nextalign, nextclade | -Identify differences between your sequences and a reference sequence used by Nextstrain | -nextclade | -nextclade | -- | Nextclade | -Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. | -Methylation analysis, Variant calling | -Genomics, Sequence analysis, Cladistics | -To update | -https://github.com/nextstrain/nextclade | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade | -2.7.0 | -nextalign | -2.14.0 | -Methylation analysis, Variant calling | -Genomics, Cladistics | -1 | -1 | -2 | -2 | -1 | -1 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -210 | -4080 | -False | -
- | nextdenovo | -nextdenovo | -String graph-based de novo assembler for long reads | -nextdenovo | -nextdenovo | -- | NextDenovo | -NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. | -De-novo assembly, Genome assembly | -Sequencing, Sequence assembly | -To update | -https://github.com/Nextomics/NextDenovo | -Assembly | -nextdenovo | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo | -https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo | -2.5.0 | -nextdenovo | -2.5.2 | -De-novo assembly, Genome assembly | -Sequencing, Sequence assembly | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -84 | -268 | -False | -
- | nonpareil | -nonpareil | -Estimate average coverage in metagenomic datasets | -nonpareil | -nonpareil | -- | nonpareil | -Estimate metagenomic coverage and sequence diversity | -Operation | -- | To update | -http://nonpareil.readthedocs.io | -Metagenomics | -nonpareil | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil | -3.1.1 | -nonpareil | -3.5.1 | -Operation | -- | 1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -5 | -142 | -False | -
- | nucleosome_prediction | -Nucleosome | -Prediction of Nucleosomes Positions on the Genome | -nucleosome_prediction | -nucleosome_prediction | -- | nucleosome_prediction | -Prediction of Nucleosomes Positions on the Genome | -Prediction and recognition, Nucleosome position prediction, Sequence analysis | -Structural genomics, Nucleic acid sites, features and motifs | -Up-to-date | -https://genie.weizmann.ac.il/software/nucleo_exe.html | -Sequence Analysis | -nucleosome_prediction | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction | -https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction | -3.0 | -nucleosome_prediction | -3.0 | -Prediction and recognition, Nucleosome position prediction, Sequence analysis | -Structural genomics, Nucleic acid sites, features and motifs | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -2 | -861 | -False | -
- | nugen_nudup | -nugen_nudup | -Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. | -nudup | -nudup | -- | NuDup | -Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. | -Duplication detection | -Sequencing | -Up-to-date | -https://github.com/tecangenomics/nudup | -SAM, Metagenomics, Sequence Analysis, Transcriptomics | -nugen_nudup | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup | -2.3.3 | -nudup | -2.3.3 | -Duplication detection | -Sequencing | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | obisindicators | -obisindicators, obis_data | -Compute biodiveristy indicators for marine data from obis | -- | - | - | - | - | - | - | To update | -https://github.com/Marie59/obisindicators | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators | -0.0.2 | -r-base | -- | - | - | 1 | -0 | -2 | -1 | -1 | -0 | -2 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -4 | -45 | -False | -
- | obitools | -obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq | -OBITools is a set of programs developed to simplify the manipulation of sequence files | -obitools | -obitools | -- | OBITools | -Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. | -Sequence analysis, Sequence analysis | -Sequence analysis, DNA, Sequencing | -Up-to-date | -http://metabarcoding.org/obitools | -Sequence Analysis | -obitools | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools | -1.2.13 | -obitools | -1.2.13 | -Sequence analysis, Sequence analysis | -Sequence analysis, DNA, Sequencing | -0 | -10 | -10 | -10 | -0 | -10 | -10 | -10 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -10 | -10 | -503 | -26251 | -False | -
- | omark | -omark | -Proteome quality assessment software | -omark | -omark | -- | OMArk | -Proteome quality assessment software | -Sequence assembly validation, Differential protein expression profiling | -Proteomics, Sequence analysis, Statistics and probability | -To update | -https://github.com/DessimozLab/OMArk | -Sequence Analysis | -omark | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark | -0.3.0 | -- | - | Sequence assembly validation, Differential protein expression profiling | -Proteomics, Sequence analysis, Statistics and probability | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | orfipy | -orfipy | -Galaxy wrapper for ORFIPY | -orfipy | -orfipy | -- | orfipy | -A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. | -Coding region prediction, Database search, Transcriptome assembly, De-novo assembly | -Computer science, RNA-Seq, Transcriptomics, Small molecules | -Up-to-date | -https://github.com/urmi-21/orfipy | -Sequence Analysis | -orfipy | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy | -0.0.4 | -orfipy | -0.0.4 | -Coding region prediction, Database search, Transcriptome assembly, De-novo assembly | -Computer science, RNA-Seq, Transcriptomics, Small molecules | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -53 | -774 | -False | -
- | orthofinder | -orthofinder_onlygroups | -Accurate inference of orthologous gene groups made easy | -OrthoFinder | -OrthoFinder | -- | OrthoFinder | -OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. | -Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment | -Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis | -Up-to-date | -https://github.com/davidemms/OrthoFinder | -Phylogenetics, Sequence Analysis | -orthofinder | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder | -2.5.5 | -orthofinder | -2.5.5 | -Genome comparison, Genome alignment | -Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -239 | -1333 | -False | -
- | peptideshaker | -fasta_cli, ident_params, peptide_shaker, search_gui | -PeptideShaker and SearchGUI | -- | - | - | - | - | - | - | To update | -http://compomics.github.io | -Proteomics | -peptideshaker | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker | -- | searchgui | -4.3.9 | -- | - | 4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -2 | -485 | -17477 | -False | -
- | pfamscan | -pfamscan | -Search a FASTA sequence against a library of Pfam HMM. | -pfamscan | -pfamscan | -- | PfamScan | -This tool is used to search a FASTA sequence against a library of Pfam HMM. | -Protein sequence analysis | -Sequence analysis | -Up-to-date | -http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ | -Sequence Analysis | -pfamscan | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan | -https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan | -1.6 | -pfam_scan | -1.6 | -Protein sequence analysis | -Sequence analysis | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -19 | -165 | -False | -
- | pharokka | -pharokka | -rapid standardised annotation tool for bacteriophage genomes and metagenomes | -pharokka | -pharokka | -- | Pharokka | -Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. | -Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly | -Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA | -To update | -https://github.com/gbouras13/pharokka | -Genome annotation | -pharokka | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka | -1.3.2 | -\n pharokka\n | -- | Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly | -Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -74 | -2565 | -False | -
- | phyloseq | -phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness | -Handling and analysis of high-throughput microbiome census data | -phyloseq | -phyloseq | -- | phyloseq | -Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. | -Deposition, Analysis, Visualisation | -Microbiology, Sequence analysis, Metagenomics | -Up-to-date | -https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html | -Metagenomics | -phyloseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq | -1.46.0 | -bioconductor-phyloseq | -1.46.0 | -Deposition, Analysis, Visualisation | -Microbiology, Sequence analysis, Metagenomics | -0 | -0 | -4 | -4 | -0 | -0 | -4 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -82 | -812 | -False | -
- | phyml | -phyml | -PhyML is a phylogeny software based on the maximum-likelihood principle. | -phyml | -phyml | -- | PhyML | -Phylogenetic estimation software using Maximum Likelihood | -Phylogenetic tree generation (maximum likelihood and Bayesian methods) | -Phylogenetics, Bioinformatics, Phylogenetics | -Up-to-date | -http://www.atgc-montpellier.fr/phyml/ | -Phylogenetics | -phyml | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml | -3.3.20220408 | -phyml | -3.3.20220408 | -- | Phylogenetics, Bioinformatics, Phylogenetics | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -104 | -1770 | -False | -
- | picrust | -picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes | -PICRUSt wrappers | -picrust | -picrust | -- | PICRUSt | -PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. | -Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding | -Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing | -To update | -https://picrust.github.io/picrust/ | -Metagenomics | -picrust | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust | -1.1.1 | -picrust | -1.1.4 | -Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding | -Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing | -0 | -6 | -5 | -6 | -0 | -6 | -5 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -45 | -1095 | -False | -
- | picrust2 | -picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions | -PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States | -picrust2 | -picrust2 | -- | PICRUSt2 | -PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. | -Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis | -Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing | -To update | -https://github.com/picrust/picrust2/wiki | -Metagenomics | -picrust2 | -iuc | -https://github.com/picrust/picrust2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 | -2.5.1 | -picrust2 | -2.5.2 | -Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis | -Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing | -0 | -7 | -7 | -0 | -0 | -7 | -7 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -7 | -0 | -88 | -1000 | -False | -
- | plasflow | -PlasFlow | -PlasFlow - Prediction of plasmid sequences in metagenomic contigs. | -plasflow | -plasflow | -- | PlasFlow | -PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. | -Sequence analysis | -Metagenomics | -Up-to-date | -https://github.com/smaegol/PlasFlow | -Sequence Analysis | -plasflow | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow | -1.1.0 | -plasflow | -1.1.0 | -Sequence analysis | -Metagenomics | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -278 | -22589 | -False | -
- | plasmidfinder | -plasmidfinder | -"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" | -PlasmidFinder | -PlasmidFinder | -- | PlasmidFinder | -PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). | -Genome assembly, Scaffolding, Multilocus sequence typing | -Whole genome sequencing, Sequence assembly, Mapping, Probes and primers | -Up-to-date | -https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ | -Sequence Analysis | -plasmidfinder | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder | -2.1.6 | -plasmidfinder | -2.1.6 | -Genome assembly, Scaffolding, Multilocus sequence typing | -Whole genome sequencing, Sequence assembly, Mapping, Probes and primers | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -8 | -22 | -False | -
- | plasmidspades | -plasmidspades | -Genome assembler for assemblying plasmid | -- | - | - | - | - | - | - | To update | -- | Assembly | -plasmidspades | -nml | -- | https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades | -1.1 | -spades | -4.0.0 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | polypolish | -polypolish | -"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." | -Polypolish | -Polypolish | -- | Polypolish | -Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. | -Genome assembly, Read mapping, Mapping assembly, Sequencing error detection | -Sequence assembly, Sequence composition, complexity and repeats, Mapping | -To update | -https://github.com/rrwick/Polypolish | -Sequence Analysis | -polypolish | -iuc | -https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish | -0.5.0 | -polypolish | -0.6.0 | -Genome assembly, Read mapping, Mapping assembly, Sequencing error detection | -Sequence assembly, Sequence composition, complexity and repeats, Mapping | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -24 | -239 | -False | -
- | prodigal | -prodigal | -A protein-coding gene prediction software tool for bacterial and archaeal genomes | -prodigal | -prodigal | -- | Prodigal | -Fast, reliable protein-coding gene prediction for prokaryotic genomes. | -Genome annotation | -Genomics, Sequence analysis | -Up-to-date | -https://github.com/hyattpd/Prodigal | -Genome annotation | -prodigal | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal | -2.6.3 | -prodigal | -2.6.3 | -Genome annotation | -Genomics, Sequence analysis | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | prokka | -prokka | -Rapid annotation of prokaryotic genomes | -prokka | -prokka | -- | Prokka | -Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. | -Gene prediction, Coding region prediction, Genome annotation | -Genomics, Model organisms, Virology | -Up-to-date | -http://github.com/tseemann/prokka | -Sequence Analysis | -prokka | -crs4 | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka | -1.14.6 | -prokka | -1.14.6 | -Coding region prediction, Genome annotation | -Genomics, Model organisms, Virology | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -1 | -3233 | -371445 | -False | -
- | promer | -promer4_substitutions | -Aligns two sets of contigs and reports amino acid substitutions between them | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/promer | -Assembly | -promer | -nml | -https://github.com/phac-nml/promer | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer | -1.2 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | proteinortho | -proteinortho, proteinortho_grab_proteins, proteinortho_summary | -Proteinortho is a tool to detect orthologous proteins/genes within different species. | -proteinortho | -proteinortho | -- | Proteinortho | -Proteinortho is a tool to detect orthologous genes within different species | -Sequence clustering, Sequence analysis | -Comparative genomics | -Up-to-date | -https://gitlab.com/paulklemm_PHD/proteinortho | -Proteomics | -proteinortho | -iuc | -https://gitlab.com/paulklemm_PHD/proteinortho | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho | -6.3.1 | -proteinortho | -6.3.1 | -Sequence clustering, Sequence analysis | -Comparative genomics | -0 | -0 | -3 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -200 | -3320 | -False | -
- | pycoqc | -pycoqc | -QC metrics for ONT Basecalling | -pycoqc | -pycoqc | -- | pycoQC | -PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. | -Sequencing quality control, Statistical calculation | -Sequence analysis, Data quality management, Sequencing | -Up-to-date | -https://github.com/tleonardi/pycoQC | -Nanopore | -pycoqc | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc | -2.5.2 | -pycoqc | -2.5.2 | -Sequencing quality control, Statistical calculation | -Sequence analysis, Data quality management, Sequencing | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -350 | -21123 | -False | -
- | pygenometracks | -pygenomeTracks | -pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. | -pygenometracks | -pygenometracks | -- | pyGenomeTracks | -reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. | -Visualisation, Formatting | -Model organisms, Imaging, Workflows | -To update | -https://github.com/deeptools/pyGenomeTracks | -Visualization | -pygenometracks | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks | -3.8 | -pygenometracks | -3.9 | -Visualisation, Formatting | -Model organisms, Imaging, Workflows | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -377 | -11332 | -False | -
- | qiime_add_on | -qiime_collapse_samples, qiime_make_otu_table | -QIIME to perform microbial community analysis | -qiime_add_on | -qiime_add_on, qiime_core | -- | qiime_add_on | -QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. | -Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control | -Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics | -To update | -http://www.qiime.org | -Metagenomics | -qiime | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on | -- | qiime | -1.9.1 | -Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control | -Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics | -0 | -0 | -2 | -2 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -68 | -1909 | -False | -
- | qiime_core | -qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file | -QIIME to perform microbial community analysis | -qiime_core | -qiime_core | -- | qiime_core | -QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. | -Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control | -Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics | -To update | -http://www.qiime.org | -Metagenomics | -qiime | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core | -- | qiime | -1.9.1 | -Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control | -Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics | -0 | -0 | -32 | -32 | -0 | -0 | -32 | -32 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -31 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -31 | -31 | -1155 | -28681 | -False | -
- | qualimap | -qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq | -- | qualimap | -qualimap | -- | QualiMap | -Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. | -Sequencing quality control | -Data quality management | -To update | -http://qualimap.bioinfo.cipf.es/ | -Sequence Analysis, Transcriptomics, SAM | -qualimap | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap | -2.2.2d | -qualimap | -2.3 | -Sequencing quality control | -Data quality management | -4 | -4 | -4 | -1 | -4 | -4 | -4 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -4 | -1328 | -664470 | -False | -
- | quast | -quast | -Quast (Quality ASsessment Tool) evaluates genome assemblies. | -quast | -quast | -- | QUAST | -QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. | -Visualisation, Sequence assembly validation | -Sequence assembly | -Up-to-date | -http://quast.bioinf.spbau.ru/ | -Assembly | -quast | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast | -5.2.0 | -quast | -5.2.0 | -Visualisation, Sequence assembly validation | -Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -3567 | -51567 | -False | -
- | quickmerge | -quickmerge | -Merge long-read and hybrid assemblies to increase contiguity | -quickmerge | -quickmerge | -- | quickmerge | -Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. | -Genome assembly, Scaffolding, De-novo assembly, Genotyping | -Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype | -Up-to-date | -https://github.com/mahulchak/quickmerge | -Assembly | -quickmerge | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge | -0.3 | -quickmerge | -0.3 | -Genome assembly, Scaffolding, De-novo assembly, Genotyping | -Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -False | -
- | rRNA | -meta_rna | -Identification of ribosomal RNA genes in metagenomic fragments. | -- | - | - | - | - | - | - | To update | -http://weizhong-lab.ucsd.edu/meta_rna/ | -RNA | -rrna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rRNA | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA | -0.1 | -hmmsearch3.0 | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | racon | -racon | -Consensus module for raw de novo DNA assembly of long uncorrected reads. | -Racon | -Racon | -- | Racon | -Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. | -Genome assembly, Mapping assembly | -Whole genome sequencing, Sequence assembly | -Up-to-date | -https://github.com/isovic/racon | -Sequence Analysis | -racon | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/racon | -https://github.com/bgruening/galaxytools/tree/master/tools/racon | -1.5.0 | -racon | -1.5.0 | -Genome assembly, Mapping assembly | -Whole genome sequencing, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -309 | -21353 | -False | -
- | rasusa | -rasusa | -Randomly subsample sequencing reads to a specified coverage | -rasusa | -rasusa | -- | rasusa | -Produces an unbiased subsample of your reads | -- | - | To update | -https://github.com/mbhall88/rasusa | -Sequence Analysis | -rasusa | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa | -0.8.0 | -rasusa | -2.0.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | raxml | -raxml | -RAxML - A Maximum Likelihood based phylogenetic inference | -raxml | -raxml | -- | RAxML | -A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. | -Sequence analysis, Phylogenetic tree analysis | -Phylogenetics, Sequence analysis | -To update | -http://www.exelixis-lab.org/web/software/raxml/ | -Phylogenetics | -raxml | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml | -8.2.12 | -raxml | -8.2.13 | -Sequence analysis | -Phylogenetics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -383 | -6808 | -False | -
- | read_it_and_keep | -read_it_and_keep | -Rapid decontamination of SARS-CoV-2 sequencing reads | -read_it_and_keep | -read_it_and_keep | -- | read_it_and_keep | -Read contamination removal | -Filtering, Genome alignment | -Pathology, Genomics | -To update | -https://github.com/GenomePathogenAnalysisService/read-it-and-keep | -Sequence Analysis | -read_it_and_keep | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep | -0.2.2 | -read-it-and-keep | -0.3.0 | -Filtering, Genome alignment | -Pathology, Genomics | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -71 | -3370 | -False | -
- | reago | -reago | -Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. | -reago | -reago | -- | REAGO | -This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. | -Sequence assembly | -Sequence assembly, RNA, Metagenomics, Microbiology | -Up-to-date | -https://github.com/chengyuan/reago-1.1 | -Metagenomics, RNA | -reago | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago | -1.1 | -reago | -1.1 | -Sequence assembly | -Sequence assembly, RNA, Metagenomics, Microbiology | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | recentrifuge | -recentrifuge | -"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." | -Recentrifuge | -Recentrifuge | -- | Recentrifuge | -Robust comparative analysis and contamination removal for metagenomics. | -Taxonomic classification, Expression analysis, Cross-assembly | -Metagenomics, Microbial ecology, Metagenomic sequencing | -Up-to-date | -https://github.com/khyox/recentrifuge | -Metagenomics | -recentrifuge | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge | -1.14.0 | -recentrifuge | -1.14.0 | -Taxonomic classification, Expression analysis, Cross-assembly | -Metagenomics, Microbial ecology, Metagenomic sequencing | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -48 | -331 | -False | -
- | repeatexplorer2 | -repeatexplorer_clustering | -Tool for annotation of repeats from unassembled shotgun reads. | -- | - | - | - | - | - | - | To update | -https://github.com/repeatexplorer/repex_tarean | -Genome annotation | -repeatexplorer2 | -gga | -https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 | -https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 | -2.3.8 | -- | - | - | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -16 | -False | -
- | roary | -roary | -Roary the pangenome pipeline | -roary | -roary | -- | Roary | -A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. | -Genome assembly | -DNA, Genomics, Mapping | -Up-to-date | -https://sanger-pathogens.github.io/Roary/ | -Sequence Analysis | -roary | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary | -3.13.0 | -roary | -3.13.0 | -Genome assembly | -DNA, Genomics, Mapping | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -656 | -12225 | -False | -
- | rseqc | -rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin | -an RNA-seq quality control package | -rseqc | -rseqc | -- | RSeQC | -Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. | -Data handling | -Sequencing | -Up-to-date | -https://code.google.com/p/rseqc/ | -Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization | -rseqc | -nilesh | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc | -5.0.3 | -rseqc | -5.0.3 | -Data handling | -Sequencing | -22 | -22 | -22 | -22 | -22 | -22 | -22 | -22 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -22 | -0 | -0 | -0 | -22 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -22 | -22 | -3206 | -133498 | -False | -
- | salmon | -alevin, salmon, salmonquantmerge | -Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. | -salmon | -salmon | -- | Salmon | -A tool for transcript expression quantification from RNA-seq data | -Sequence composition calculation, RNA-Seq quantification, Gene expression analysis | -RNA-Seq, Gene expression, Transcriptomics | -To update | -https://github.com/COMBINE-lab/salmon | -Sequence Analysis, RNA, Transcriptomics | -- | bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/salmon | -https://github.com/bgruening/galaxytools/tree/master/tools/salmon | -1.10.1 | -salmon | -1.10.3 | -Sequence composition calculation, RNA-Seq quantification, Gene expression analysis | -RNA-Seq, Transcriptomics | -2 | -1 | -3 | -1 | -2 | -1 | -3 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -969 | -61937 | -False | -
- | sarscov2formatter | -sarscov2formatter | -sarscov2formatter custom script | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/nickeener/sarscov2formatter | -Sequence Analysis | -sarscov2formatter | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter | -1.0 | -sarscov2formatter | -1.0 | -- | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -7 | -173 | -False | -
- | sarscov2summary | -sarscov2summary | -sarscov2summary custom script | -- | - | - | - | - | - | - | To update | -https://github.com/nickeener/sarscov2summary | -Sequence Analysis | -sarscov2summary | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary | -0.1 | -sarscov2summary | -0.5 | -- | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -140 | -False | -
- | scoary | -scoary | -Scoary calculates the assocations between all genes in the accessory genome and the traits. | -scoary | -scoary | -- | Scoary | -Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. | -Analysis | -Genotype and phenotype, Model organisms, GWAS study, Functional genomics | -Up-to-date | -https://github.com/AdmiralenOla/Scoary | -Metagenomics | -scoary | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary | -1.6.16 | -scoary | -1.6.16 | -Analysis | -Genotype and phenotype, Model organisms, GWAS study, Functional genomics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -61 | -676 | -False | -
- | semibin | -semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train | -SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks | -semibin | -semibin | -- | SemiBin | -Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. | -Sequence assembly, Read binning | -Metagenomics, Machine learning, Microbial ecology, Sequence assembly | -To update | -https://semibin.readthedocs.io/en/latest/ | -Metagenomics | -semibin | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin | -2.0.2 | -semibin | -2.1.0 | -Sequence assembly, Read binning | -Metagenomics, Machine learning, Microbial ecology, Sequence assembly | -0 | -0 | -6 | -1 | -0 | -0 | -6 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -0 | -39 | -542 | -False | -
- | seqkit | -seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate | -A cross-platform and ultrafast toolkit for FASTA/Q file manipulation | -seqkit | -seqkit | -- | seqkit | -FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. | -DNA transcription, Sequence trimming, DNA translation, Sequence conversion | -Database management, Sequence analysis | -Up-to-date | -https://bioinf.shenwei.me/seqkit/ | -Sequence Analysis | -seqkit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit | -2.8.2 | -seqkit | -2.8.2 | -DNA transcription, Sequence trimming, DNA translation | -Database management, Sequence analysis | -0 | -2 | -3 | -2 | -0 | -2 | -3 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -129 | -1964 | -False | -
- | seqprep | -seqprep | -Tool for merging paired-end Illumina reads and trimming adapters. | -seqprep | -seqprep | -- | SeqPrep | -Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. | -Nucleic acid design | -Genomics, Sequence assembly, Sequencing, Probes and primers | -Up-to-date | -https://github.com/jstjohn/SeqPrep | -Fastq Manipulation, Sequence Analysis | -seqprep | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep | -1.3.2 | -seqprep | -1.3.2 | -Nucleic acid design | -Genomics, Sequence assembly, Sequencing, Probes and primers | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | seqsero2 | -seqsero2 | -Salmonella serotype prediction from genome sequencing data | -seqsero2 | -seqsero2 | -- | SeqSero2 | -rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode) | -Genome indexing, Antimicrobial resistance prediction, Genome alignment | -Whole genome sequencing, Sequence assembly, Genomics | -Up-to-date | -https://github.com/denglab/SeqSero2 | -Sequence Analysis | -seqsero2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 | -1.3.1 | -seqsero2 | -1.3.1 | -Genome indexing, Antimicrobial resistance prediction, Genome alignment | -Whole genome sequencing, Sequence assembly, Genomics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -12 | -False | -
- | shorah | -shorah_amplicon | -Reconstruct haplotypes using ShoRAH in amplicon mode | -shorah | -shorah | -- | ShoRAH | -Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. | -Haplotype mapping, Variant calling | -Metagenomics, Sequencing, Genetics | -To update | -https://github.com/cbg-ethz/shorah/blob/master/README.md | -Sequence Analysis | -shorah_amplicon | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah | -1.1.3 | -shorah | -1.99.2 | -Haplotype mapping, Variant calling | -Metagenomics, Sequencing, Genetics | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | shovill | -shovill | -Faster de novo assembly pipeline based around Spades | -shovill | -shovill | -- | shovill | -Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. | -Genome assembly | -Genomics, Microbiology, Sequence assembly | -Up-to-date | -https://github.com/tseemann/shovill | -Assembly | -shovill | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill | -1.1.0 | -shovill | -1.1.0 | -Genome assembly | -Genomics, Microbiology, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1008 | -41600 | -False | -
- | sistr_cmd | -sistr_cmd | -SISTR in silico serotyping tool | -- | - | - | - | - | - | - | To update | -https://github.com/phac-nml/sistr_cmd | -Sequence Analysis | -sistr_cmd | -nml | -- | https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd | -1.1.1 | -sistr_cmd | -1.1.2 | -- | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -133 | -2489 | -False | -
- | smallgenomeutilities | -smgu_frameshift_deletions_checks | -Set of utilities for manipulating small viral genome data. | -v-pipe | -v-pipe | -- | V-pipe | -Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. | -Read pre-processing, Sequence alignment, Genetic variation analysis | -Genomics, Population genetics, Workflows, Virology, Sequencing | -Up-to-date | -https://github.com/cbg-ethz/smallgenomeutilities | -Sequence Analysis | -smallgenomeutilities | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities | -0.4.1 | -smallgenomeutilities | -0.4.1 | -Read pre-processing, Sequence alignment, Genetic variation analysis | -Genomics, Population genetics, Workflows, Virology, Sequencing | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -6 | -121 | -False | -
- | smalt | -smalt | -SMALT aligns DNA sequencing reads with a reference genome. | -- | - | - | - | - | - | - | Up-to-date | -http://www.sanger.ac.uk/science/tools/smalt-0 | -Sequence Analysis | -smalt | -nml | -https://sourceforge.net/projects/smalt/ | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt | -0.7.6 | -smalt | -0.7.6 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | snap | -snap, snap_training | -SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. | -snap | -snap | -- | SNAP | -The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. | -Gene prediction | -DNA, DNA polymorphism, Genetics | -Up-to-date | -https://github.com/KorfLab/SNAP | -Sequence Analysis | -snap | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap | -2013_11_29 | -snap | -2013_11_29 | -Gene prediction | -DNA polymorphism, Genetics | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -133 | -1349 | -False | -
- | snippy | -snippy_core, snippy, snippy_clean_full_aln | -Contains the snippy tool for characterising microbial snps | -snippy | -snippy | -- | snippy | -Rapid haploid variant calling and core SNP phylogeny generation. | -Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling | -Genomics, Model organisms, DNA polymorphism, Phylogenetics | -To update | -https://github.com/tseemann/snippy | -Sequence Analysis | -snippy | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy | -- | snippy | -4.6.0 | -Phylogenetic tree visualisation, Variant calling | -Genomics, Model organisms, DNA polymorphism, Phylogenetics | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -2 | -1372 | -105708 | -False | -
- | sonneityping | -sonneityping | -Scripts for parsing Mykrobe predict results for Shigella sonnei. | -sonneityping | -sonneityping | -- | sonneityping | -Scripts for parsing Mykrobe predict results for Shigella sonnei. | -Antimicrobial resistance prediction, Variant calling, Genotyping | -Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics | -Up-to-date | -https://github.com/katholt/sonneityping | -Sequence Analysis | -sonneityping | -iuc | -https://github.com/katholt/sonneityping | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping | -20210201 | -sonneityping | -20210201 | -Antimicrobial resistance prediction, Variant calling, Genotyping | -Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -1 | -False | -
- | sortmerna | -bg_sortmerna | -SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. | -sortmerna | -sortmerna | -- | SortMeRNA | -Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. | -Sequence similarity search, Sequence comparison, Sequence alignment analysis | -Metatranscriptomics, Metagenomics | -To update | -http://bioinfo.lifl.fr/RNA/sortmerna/ | -RNA | -sortmerna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna | -4.3.6 | -sortmerna | -4.3.7 | -Sequence similarity search, Sequence alignment analysis | -Metatranscriptomics, Metagenomics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -376 | -18183 | -False | -
- | spades | -spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades | -SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. | -spades | -rnaspades, spades, biosyntheticspades, metaspades, rnaviralspades, plasmidspades, coronaspades, metaviralspades, metaplasmidspades | -- | SPAdes | -St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. | -Genome assembly | -Sequence assembly | -To update | -https://github.com/ablab/spades | -Assembly, RNA, Metagenomics | -spades | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades | -3.15.5 | -spades | -4.0.0 | -Genome assembly | -Sequence assembly | -9 | -9 | -9 | -9 | -9 | -9 | -9 | -9 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -3 | -8 | -0 | -0 | -2 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -9 | -3 | -3547 | -72953 | -False | -
- | spotyping | -spotyping | -SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads | -spotyping | -spotyping | -- | SpoTyping | -Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. | -Variant pattern analysis | -Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation | -Up-to-date | -https://github.com/xiaeryu/SpoTyping-v2.0 | -Sequence Analysis | -spotyping | -iuc | -https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping | -2.1 | -spotyping | -2.1 | -Variant pattern analysis | -Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -12 | -1278 | -False | -
- | sr_bowtie | -bowtieForSmallRNA | -bowtie wrapper tool to align small RNA sequencing reads | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -RNA, Next Gen Mappers | -sr_bowtie | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie | -https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie | -2.3.0 | -bowtie | -1.3.1 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | srst2 | -srst2 | -Short Read Sequence Typing for Bacterial Pathogens | -- | - | - | - | - | - | - | To update | -- | Sequence Analysis | -srst2 | -nml | -- | https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 | -0.3.7 | -srst2 | -0.2.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -22 | -205 | -False | -
- | srst2 | -srst2 | -SRST2 Short Read Sequence Typing for Bacterial Pathogens | -srst2 | -srst2 | -- | srst2 | -Short Read Sequence Typing for Bacterial Pathogens | -Multilocus sequence typing | -Whole genome sequencing, Public health and epidemiology | -To update | -http://katholt.github.io/srst2/ | -Metagenomics | -srst2 | -iuc | -https://github.com/katholt/srst2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 | -0.2.0 | -samtools | -1.20 | -Multilocus sequence typing | -Whole genome sequencing, Public health and epidemiology | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -22 | -205 | -False | -
- | staramr | -staramr_search | -Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/phac-nml/staramr | -Sequence Analysis | -staramr | -nml | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr | -0.10.0 | -staramr | -0.10.0 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -889 | -12673 | -False | -
- | stringmlst | -stringmlst | -Rapid and accurate identification of the sequence type (ST) | -- | - | - | - | - | - | - | To update | -- | Sequence Analysis | -stringmlst | -nml | -- | https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst | -1.1.0 | -stringMLST | -0.6.3 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | structure | -structure | -for using multi-locus genotype data to investigate population structure. | -structure | -structure | -- | Structure | -The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. | -Genetic variation analysis | -Population genetics | -Up-to-date | -- | Phylogenetics, Variant Analysis | -structure | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure | -2.3.4 | -structure | -2.3.4 | -Genetic variation analysis | -Population genetics | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -59 | -2623 | -False | -
- | suite_qiime2__alignment | -qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-alignment | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -6 | -13 | -False | -
- | suite_qiime2__composition | -qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-composition | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 4 | -4 | -4 | -2 | -4 | -4 | -4 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -2 | -5 | -False | -
- | suite_qiime2__cutadapt | -qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-cutadapt | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -5 | -67 | -False | -
- | suite_qiime2__dada2 | -qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single | -- | - | - | - | - | - | - | - | To update | -http://benjjneb.github.io/dada2/ | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -31 | -202 | -False | -
- | suite_qiime2__deblur | -qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats | -- | - | - | - | - | - | - | - | To update | -https://github.com/biocore/deblur | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -9 | -73 | -False | -
- | suite_qiime2__demux | -qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-demux | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 6 | -6 | -6 | -6 | -6 | -6 | -6 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -0 | -26 | -114 | -False | -
- | suite_qiime2__diversity | -qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-diversity | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 21 | -21 | -21 | -21 | -21 | -21 | -21 | -21 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -21 | -0 | -43 | -168 | -False | -
- | suite_qiime2__diversity_lib | -qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-diversity-lib | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 12 | -12 | -12 | -12 | -12 | -12 | -12 | -12 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -12 | -0 | -4 | -4 | -False | -
- | suite_qiime2__emperor | -qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot | -- | - | - | - | - | - | - | - | To update | -http://emperor.microbio.me | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -2 | -6 | -False | -
- | suite_qiime2__feature_classifier | -qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-feature-classifier | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 10 | -10 | -10 | -10 | -10 | -10 | -10 | -10 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -10 | -0 | -48 | -263 | -False | -
- | suite_qiime2__feature_table | -qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-feature-table | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 17 | -17 | -17 | -17 | -17 | -17 | -17 | -17 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -17 | -0 | -59 | -213 | -False | -
- | suite_qiime2__fragment_insertion | -qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-fragment-insertion | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -6 | -20 | -False | -
- | suite_qiime2__longitudinal | -qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-longitudinal | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 11 | -11 | -11 | -11 | -11 | -11 | -11 | -11 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -11 | -0 | -6 | -14 | -False | -
- | suite_qiime2__metadata | -qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-metadata | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -40 | -232 | -False | -
- | suite_qiime2__phylogeny | -qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-phylogeny | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 12 | -12 | -12 | -12 | -12 | -12 | -12 | -12 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -12 | -0 | -12 | -37 | -False | -
- | suite_qiime2__quality_control | -qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-quality-control | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 6 | -6 | -6 | -6 | -6 | -6 | -6 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -0 | -0 | -0 | -False | -
- | suite_qiime2__quality_filter | -qiime2__quality_filter__q_score | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-quality-filter | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -2 | -13 | -False | -
- | suite_qiime2__rescript | -qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment | -- | - | - | - | - | - | - | - | To update | -https://github.com/nbokulich/RESCRIPt | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | suite_qiime2__sample_classifier | -qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-sample-classifier | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 15 | -15 | -15 | -15 | -15 | -15 | -15 | -15 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -15 | -0 | -1 | -1 | -False | -
- | suite_qiime2__taxa | -qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-taxa | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -22 | -172 | -False | -
- | suite_qiime2__vsearch | -qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref | -- | - | - | - | - | - | - | - | To update | -https://github.com/qiime2/q2-vsearch | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch | -2024.5.0+q2galaxy.2024.5.0 | -- | - | - | - | 8 | -8 | -8 | -7 | -8 | -8 | -8 | -7 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -8 | -0 | -8 | -16 | -False | -
- | suite_qiime2_core | -- | - | - | - | - | - | - | - | - | To update | -- | Statistics, Metagenomics, Sequence Analysis | -- | q2d2 | -- | https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core | -- | - | - | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | suite_qiime2_core__tools | -qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq | -- | - | - | - | - | - | - | - | To update | -https://qiime2.org | -Metagenomics, Sequence Analysis, Statistics | -- | q2d2 | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools | -https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools | -2024.5.0+dist.he540b0b0 | -- | - | - | - | 2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -124 | -7087 | -False | -
- | t2ps | -Draw_phylogram | -Draw phylogeny | -t2ps | -t2ps | -- | Draw phylogeny | -"Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format." - Galaxy tool wrapper | -Phylogenetic tree visualisation | -Phylogenomics | -To update | -https://bitbucket.org/natefoo/taxonomy | -Metagenomics | -t2ps | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps | -https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps | -1.0.0 | -taxonomy | -0.10.0 | -Phylogenetic tree visualisation | -Phylogenomics | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -31 | -457 | -False | -
- | t2t_report | -t2t_report | -Summarize taxonomy | -- | - | - | - | - | - | - | To update | -https://bitbucket.org/natefoo/taxonomy | -Metagenomics | -t2t_report | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report | -https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report | -1.0.0 | -taxonomy | -0.10.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -26 | -947 | -False | -
- | t_coffee | -t_coffee | -T-Coffee | -- | - | - | - | - | - | - | To update | -http://www.tcoffee.org/ | -Sequence Analysis | -t_coffee | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee | -13.45.0.4846264 | -t-coffee | -13.46.0.919e8c6b | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -70 | -8690 | -False | -
- | taxonomy_krona_chart | -taxonomy_krona_chart | -Krona pie chart from taxonomic profile | -krona | -krona | -- | Krona | -Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). | -Visualisation | -Metagenomics | -To update | -http://sourceforge.net/projects/krona/ | -Assembly | -taxonomy_krona_chart | -crs4 | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart | -2.7.1+galaxy0 | -krona | -2.8.1 | -Visualisation | -Metagenomics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -1 | -1801 | -27426 | -False | -
- | tb-profiler | -tb_profiler_profile | -Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. | -tb-profiler | -tb-profiler | -- | tb-profiler | -A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). | -Antimicrobial resistance prediction | -- | Up-to-date | -https://github.com/jodyphelan/TBProfiler | -Sequence Analysis | -tbprofiler | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler | -6.2.1 | -tb-profiler | -6.2.1 | -Antimicrobial resistance prediction | -- | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -198 | -5161 | -False | -
- | tooldistillator | -tooldistillator, tooldistillator_summarize | -ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files | -tooldistillator | -tooldistillator | -- | ToolDistillator | -ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. | -Data handling, Parsing | -Microbiology, Bioinformatics, Sequence analysis | -Up-to-date | -https://gitlab.com/ifb-elixirfr/abromics/tooldistillator | -Sequence Analysis | -tooldistillator | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator | -0.8.5.0 | -tooldistillator | -0.8.5.0 | -Parsing | -Microbiology, Bioinformatics, Sequence analysis | -2 | -0 | -2 | -2 | -2 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | transit | -gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps | -TRANSIT | -transit | -transit | -- | TRANSIT | -A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. | -Transposon prediction | -DNA, Sequencing, Mobile genetic elements | -To update | -https://github.com/mad-lab/transit/ | -Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit | -3.0.2 | -transit | -3.2.3 | -Transposon prediction | -DNA, Sequencing, Mobile genetic elements | -5 | -5 | -5 | -0 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -84 | -907 | -False | -
- | transtermhp | -transtermhp | -Finds rho-independent transcription terminators in bacterial genomes | -transtermhp | -transtermhp | -- | TransTermHP | -TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator | -Transcriptional regulatory element prediction | -Transcription factors and regulatory sites | -To update | -https://transterm.cbcb.umd.edu | -Sequence Analysis | -transtermhp | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp | -- | transtermhp | -2.09 | -Transcriptional regulatory element prediction | -Transcription factors and regulatory sites | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -5 | -229 | -False | -
- | trim_galore | -trim_galore | -Trim Galore adaptive quality and adapter trimmer | -trim_galore | -trim_galore | -- | Trim Galore | -A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. | -Sequence trimming, Primer removal, Read pre-processing | -Sequence analysis | -To update | -http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ | -Sequence Analysis, Fastq Manipulation | -trim_galore | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore | -https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore | -0.6.7 | -trim-galore | -0.6.10 | -Sequence trimming, Primer removal, Read pre-processing | -Sequence analysis | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -2334 | -238699 | -False | -
- | trycycler | -trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample | -Trycycler toolkit wrappers | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/rrwick/Trycycler | -Assembly | -trycycler | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler | -0.5.5 | -trycycler | -0.5.5 | -- | - | 0 | -5 | -5 | -5 | -0 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -147 | -8942 | -False | -
- | unicycler | -unicycler | -Unicycler is a hybrid assembly pipeline for bacterial genomes. | -unicycler | -unicycler | -- | Unicycler | -A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. | -Genome assembly, Aggregation | -Microbiology, Genomics, Sequencing, Sequence assembly | -Up-to-date | -https://github.com/rrwick/Unicycler | -Assembly | -unicycler | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler | -0.5.0 | -unicycler | -0.5.0 | -Genome assembly, Aggregation | -Microbiology, Genomics, Sequencing, Sequence assembly | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1558 | -65732 | -False | -
- | unipept | -unipept | -Unipept retrieves metaproteomics information | -unipept | -unipept | -- | Unipept | -Metaproteomics data analysis with a focus on interactive data visualizations. | -Prediction and recognition, Visualisation | -Proteomics, Proteogenomics, Biodiversity, Workflows | -To update | -https://github.com/galaxyproteomics/tools-galaxyp | -Proteomics | -unipept | -galaxyp | -https://unipept.ugent.be/apidocs | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept | -4.5.1 | -python | -- | Prediction and recognition, Visualisation | -Proteomics, Proteogenomics, Biodiversity, Workflows | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -115 | -5005 | -False | -
- | uniprotxml_downloader | -uniprotxml_downloader | -Download UniProt proteome in XML or fasta format | -- | - | - | - | - | - | - | To update | -- | Proteomics | -uniprotxml_downloader | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader | -2.4.0 | -requests | -- | - | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -79 | -1360 | -False | -
- | usher | -usher_matutils, usher | -UShER toolkit wrappers | -usher | -usher | -- | usher | -The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. | -Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) | -Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics | -To update | -https://github.com/yatisht/usher | -Phylogenetics | -usher | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher | -0.2.1 | -usher | -0.6.3 | -Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) | -Cladistics, Genotype and phenotype, Phylogenomics | -0 | -0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -5 | -1060 | -False | -
- | valet | -valet | -A pipeline for detecting mis-assemblies in metagenomic assemblies. | -valet | -valet | -- | VALET | -VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. | -Sequence assembly, Sequence assembly visualisation | -Metagenomics, Sequence assembly | -To update | -https://github.com/marbl/VALET | -Metagenomics | -valet | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet | -- | valet | -1.0 | -Sequence assembly, Sequence assembly visualisation | -Metagenomics, Sequence assembly | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -20 | -637 | -False | -
- | vapor | -vapor | -Classify Influenza samples from raw short read sequence data | -vapor | -vapor | -- | VAPOR | -VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. | -Data retrieval, De-novo assembly, Read mapping | -Whole genome sequencing, Mapping, Sequence assembly | -Up-to-date | -https://github.com/connor-lab/vapor | -Sequence Analysis | -vapor | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor | -1.0.2 | -vapor | -1.0.2 | -Data retrieval, De-novo assembly, Read mapping | -Whole genome sequencing, Mapping, Sequence assembly | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -94 | -3164 | -False | -
- | varvamp | -varvamp | -Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses | -varvamp | -varvamp | -- | varVAMP | -variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. | -PCR primer design | -Virology | -Up-to-date | -https://github.com/jonas-fuchs/varVAMP/ | -Sequence Analysis | -varvamp | -iuc | -https://github.com/jonas-fuchs/varVAMP | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp | -1.2.0 | -varvamp | -1.2.0 | -PCR primer design | -Virology | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | vegan | -vegan_diversity, vegan_fisher_alpha, vegan_rarefaction | -an R package fo community ecologist | -vegan | -vegan | -- | vegan | -Ordination methods, diversity analysis and other functions for community and vegetation ecologists | -Standardisation and normalisation, Analysis | -Ecology, Phylogenetics, Environmental science | -To update | -https://cran.r-project.org/package=vegan | -Metagenomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan | -2.4-3 | -r-vegan | -2.3_4 | -Standardisation and normalisation, Analysis | -Ecology, Phylogenetics, Environmental science | -3 | -0 | -3 | -0 | -3 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -74 | -2020 | -False | -
- | velvet | -velvetg, velveth | -de novo genomic assembler specially designed for short read sequencing technologies | -velvet | -velvet | -- | Velvet | -A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. | -Formatting, De-novo assembly | -Sequence assembly | -To update | -https://www.ebi.ac.uk/~zerbino/velvet/ | -Assembly | -velvet | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet | -- | velvet | -1.2.10 | -Formatting, De-novo assembly | -Sequence assembly | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -2083 | -25420 | -False | -
- | velvet_optimiser | -velvetoptimiser | -Automatically optimize Velvet assemblies | -velvetoptimiser | -velvetoptimiser | -- | VelvetOptimiser | -This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. | -Optimisation and refinement, Sequence assembly | -Genomics, Sequence assembly | -To update | -- | Assembly | -velvetoptimiser | -simon-gladman | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser | -2.2.6+galaxy2 | -velvet | -1.2.10 | -Optimisation and refinement, Sequence assembly | -Genomics, Sequence assembly | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -255 | -4741 | -False | -
- | virAnnot | -virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv | -virAnnot wrappers | -virannot | -virannot | -- | virAnnot | -VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project "Plant Health Bioinformatics Network". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy. | -Sequence annotation, Sequence clustering, Sequence cluster visualisation | -Metagenomics, Virology, Microbial ecology | -To update | -https://github.com/marieBvr/virAnnot | -Metagenomics | -virannot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot | -1.0.0+galaxy0 | -biopython | -1.70 | -Sequence annotation, Sequence clustering, Sequence cluster visualisation | -Metagenomics, Virology, Microbial ecology | -0 | -0 | -3 | -3 | -0 | -0 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -False | -
- | vsearch | -vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting | -VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. | -vsearch | -vsearch | -- | VSEARCH | -High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. | -DNA mapping, Chimera detection | -Metagenomics, Sequence analysis | -To update | -https://github.com/torognes/vsearch | -Sequence Analysis | -vsearch | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch | -2.8.3 | -vsearch | -2.28.1 | -DNA mapping, Chimera detection | -Metagenomics, Sequence analysis | -8 | -8 | -8 | -8 | -8 | -8 | -8 | -8 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -8 | -8 | -0 | -0 | -0 | -0 | -0 | -0 | -8 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -8 | -8 | -182 | -8507 | -False | -
- | wtdbg | -wtdbg | -WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. | -wtdbg2 | -wtdbg2 | -- | wtdbg2 | -Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. | -Genome assembly, De-novo assembly | -Sequence assembly, Sequencing | -Up-to-date | -https://github.com/ruanjue/wtdbg2 | -Assembly | -wtdbg | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg | -https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg | -2.5 | -wtdbg | -2.5 | -Genome assembly, De-novo assembly | -Sequence assembly, Sequencing | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -116 | -1660 | -False | -
Expand | -Topic | -Title | -Link | -EDAM topic | -EDAM operation | -Creation | -Last modification | -Version | -Tutorial | -Slides | -Video | -Workflows | -Tools | -Servers with precise tool versions | -Servers with tool but different versions | -Feedback number | -Feedback mean note | -Visitors | -Page views | -Visit duration | -Video views | -
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
- | Assembly | -Making sense of a newly assembled genome | -https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html | -Sequence assembly, Genomics, Microbiology | -Genome visualisation, Sequence alignment, Read mapping, Sequence visualisation, Mapping | -2018-06-14 | -2024-03-11 | -86 | -True | -False | -False | -True | -Cut1, tp_replace_in_line, mergeCols1, tp_replace_in_column, fasta_filter_by_length, Grep1, cat1, circos_aln_to_links, jbrowse, fasta_compute_length, collapse_dataset, random_lines1, bedtools_sortbed, lastz_wrapper_2, addValue, circos, join1, Filter1, bedtools_intersectbed, bedtools_complementbed, upload1, tp_sed_tool, tp_cat, datamash_ops, tp_sort_header_tool, circos_interval_to_tiles, tp_grep_tool | -- | - | 1 | -2.0 | -5828 | -11935 | -3.033333 | -0 | -
- | Assembly | -Assembly of metagenomic sequencing data | -https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html | -Metagenomics, Sequence assembly | -Sequence composition calculation, Genome assembly, Visualisation, Primer removal, Sequence assembly visualisation, Sequence file editing, Read mapping, Statistical calculation, Data handling, Sequence contamination filtering, Local alignment, Sequence alignment analysis, Variant calling, Sequencing quality control, Read pre-processing, Sequence assembly validation, Formatting, Sequence trimming | -2024-06-24 | -2024-06-24 | -0 | -True | -False | -False | -True | -filter_tabular, bandage_image, metaspades, megahit, quast, cutadapt, tp_cat, ngsutils_bam_filter, megahit_contig2fastg, random_lines1, bamtools, bowtie2, bandage_info, collection_column_join, coverm_contig, seqtk_subseq, fastqc, bg_uniq | -- | UseGalaxy.cz, UseGalaxy.eu | -0 | -- | 1 | -1 | -0.000000 | -0 | -
- | Assembly | -Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data | -https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html | -Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology | -Sequence assembly visualisation, Sequence composition calculation, Sequence contamination filtering, Genome assembly, Statistical calculation, Sequencing quality control, Visualisation, Sequence assembly validation | -2021-03-24 | -2024-03-11 | -28 | -True | -False | -False | -True | -bandage_image, upload1, quast, bandage_info, fastqc, fastp, shovill | -UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) | -Galaxy@AuBi, GalaxyTrakr, UseGalaxy.no | -8 | -4.5 | -6115 | -9890 | -3.733333 | -0 | -
- | Assembly | -Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) | -https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html | -Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance | -De-novo assembly, Sequence composition calculation, Genome assembly, Sequencing error detection, Visualisation, Sequencing quality control, Mapping assembly, Sequence assembly visualisation, Sequence assembly validation, Cross-assembly, Box-Whisker plot plotting, Scatter plot plotting, Filtering, Read mapping, Statistical calculation, Sequence alignment, Sequence contamination filtering | -2021-03-24 | -2024-03-13 | -35 | -True | -False | -False | -True | -flye, nanoplot, bandage_image, polypolish, upload1, quast, porechop, CONVERTER_bz2_to_uncompressed, bwa_mem2, filtlong, fastqc, fastp | -UseGalaxy.eu | -UseGalaxy.cz | -2 | -4.0 | -6353 | -9777 | -3.416667 | -0 | -
- | Assembly | -Unicycler Assembly | -https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html | -Sequence assembly, Genomics, Microbiology | -Sequence composition calculation, Genome assembly, Validation, Coding region prediction, Sequencing quality control, Visualisation, Sequence assembly validation, Statistical calculation, Gene prediction, Aggregation, Genome annotation | -2017-10-11 | -2024-03-11 | -61 | -True | -True | -False | -True | -quast, prokka, unicycler, multiqc, fastqc | -UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au | -GalaxyTrakr, HyPhy HIV NGS Tools, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no | -8 | -3.75 | -1994916 | -5552489 | -4.566667 | -0 | -
- | Ecology | -Checking expected species and contamination in bacterial isolate | -https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html | -Whole genome sequencing, Genomics, Microbiology, Microbial ecology | -Statistical calculation, Cross-assembly, Taxonomic classification, Expression analysis | -2024-03-04 | -2024-04-04 | -5 | -True | -False | -False | -True | -kraken2, recentrifuge, upload1, est_abundance | -UseGalaxy.eu, UseGalaxy.fr | -Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) | -1 | -5.0 | -165 | -226 | -4.866667 | -0 | -
- | Evolution | -Tree thinking for tuberculosis evolution and epidemiology | -https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html | -Genomics, Microbiology, Phylogeny, Infectious disease | -Sequence analysis, Phylogenetic tree analysis | -2022-03-16 | -2023-02-15 | -19 | -True | -False | -False | -True | -raxml, interactive_tool_rstudio, upload1 | -UseGalaxy.eu | -UseGalaxy.fr, UseGalaxy.org (Main) | -6 | -4.333333 | -1211 | -1857 | -2.266667 | -0 | -
- | Evolution | -Identifying tuberculosis transmission links: from SNPs to transmission clusters | -https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html | -Genomics, Microbiology, Infectious disease, DNA polymorphism | -Antimicrobial resistance prediction, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling | -2022-03-16 | -2024-03-12 | -15 | -True | -False | -False | -True | -snippy, tb_variant_filter, tp_replace_in_line, trimmomatic, bcftools_consensus, snp_sites, tp_sed_tool, addName, tp_cat, upload1, collapse_dataset, Grep1, __MERGE_COLLECTION__, tp_easyjoin_tool, tb_profiler_profile, samtools_view, tp_grep_tool, snp_dists | -UseGalaxy.eu | -UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) | -7 | -4.0 | -1377 | -2211 | -3.183333 | -0 | -
- | Genome Annotation | -Genome annotation with Prokka | -https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html | -Genomics, Microbiology, Gene and protein families, Sequence analysis | -Genome annotation, Coding region prediction, Gene prediction, Genome visualisation | -2018-03-06 | -2024-05-29 | -43 | -True | -True | -True | -True | -prokka, jbrowse | -UseGalaxy.eu, UseGalaxy.org (Main) | -Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au | -17 | -3.764706 | -1999341 | -5560175 | -4.316667 | -0 | -
- | Genome Annotation | -Bacterial Genome Annotation | -https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html | -Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements | -Structural variation detection, Genome assembly, Nucleic acid feature detection, Protein feature detection, Scaffolding, Multilocus sequence typing, Sequence motif recognition, Genome visualisation, Genome annotation | -2024-02-01 | -2024-03-13 | -8 | -True | -False | -False | -True | -tp_tail_tool, upload1, bakta, isescan, Grouping1, tp_replace_in_column, tbl2gff3, plasmidfinder, integron_finder, jbrowse | -Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr | -- | 1 | -1.0 | -1237 | -1630 | -2.483333 | -0 | -
- | Genome Annotation | -Identification of AMR genes in an assembled bacterial genome | -https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html | -Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance | -Genome annotation, Genome visualisation, Read mapping | -2024-01-23 | -2024-03-13 | -9 | -True | -False | -False | -True | -upload1, staramr_search, bakta, Grep1, bowtie2, tbl2gff3, jbrowse | -UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr | -Galaxy@AuBi | -0 | -- | 726 | -1061 | -3.066667 | -0 | -
- | Genome Annotation | -Refining Genome Annotations with Apollo (prokaryotes) | -https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html | -Genomics, Microbiology, Gene and protein families, Sequence analysis | -Genome visualisation | -2021-06-04 | -2024-05-29 | -40 | -True | -True | -True | -True | -iframe, create_or_update, list_organism, create_account, jbrowse | -- | UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no | -5 | -4.6 | -1757138 | -4755339 | -5.016667 | -0 | -
- | Genome Annotation | -Comparative gene analysis in unannotated genomes | -https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html | -Genomics, Gene and protein families, Sequence analysis, Phylogeny | -De-novo assembly, Sequence alignment analysis, Multiple sequence alignment, Coding region prediction, Phylogenetic tree generation, Transcriptome assembly, Database search | -2022-09-08 | -2024-03-18 | -30 | -True | -False | -False | -True | -Add_a_column1, gops_intersect_1, Cut1, orfipy, bg_diamond_view, tp_split_on_column, bg_diamond, tab2fasta, rbc_mafft, collapse_dataset, cat1, regexColumn1, join1, rapidnj, Filter1, bg_diamond_makedb | -UseGalaxy.eu, UseGalaxy.org (Main) | -UseGalaxy.cz | -0 | -- | 910 | -1395 | -3.116667 | -0 | -
- | Genome Annotation | -Essential genes detection with Transposon insertion sequencing | -https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html | -Genomics, Microbiology, Sequence analysis, Mobile genetic elements | -Transposon prediction, Primer removal, Read pre-processing, Sequence trimming | -2019-07-02 | -2024-03-15 | -52 | -True | -True | -False | -True | -Add_a_column1, Cut1, bowtie_wrapper, transit_gumbel, cutadapt, gff_to_prot, tp_sort_header_tool, __EXTRACT_DATASET__, deeptools_bam_coverage, tp_easyjoin_tool, bg_find_subsequences, Filter1 | -UseGalaxy.no | -UseGalaxy.cz, UseGalaxy.eu | -4 | -4.5 | -1990676 | -5545573 | -4.250000 | -0 | -
- | Genome Annotation | -Genome annotation with Prokka | -https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html | -Genomics, Microbiology, Gene and protein families, Sequence analysis | -Genome annotation, Coding region prediction, Gene prediction, Genome visualisation | -2018-03-06 | -2024-05-29 | -43 | -True | -True | -True | -True | -prokka, jbrowse | -UseGalaxy.eu, UseGalaxy.org (Main) | -Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au | -17 | -3.764706 | -1999341 | -5560176 | -4.316667 | -0 | -
- | Variant Analysis | -Microbial Variant Calling | -https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html | -Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation | -Genome visualisation, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling | -2018-02-26 | -2024-03-14 | -36 | -True | -False | -False | -True | -snippy, jbrowse | -UseGalaxy.eu, UseGalaxy.org (Main) | -GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au | -12 | -4.416667 | -11631 | -19648 | -1.983333 | -0 | -
- | Assembly | -Making sense of a newly assembled genome | -https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html | -Sequence assembly, Genomics, Microbiology | -Genome visualisation, Sequence alignment, Read mapping, Sequence visualisation, Mapping | -2018-06-14 | -2024-03-11 | -86 | -True | -False | -False | -True | -Cut1, tp_replace_in_line, mergeCols1, tp_replace_in_column, fasta_filter_by_length, Grep1, cat1, circos_aln_to_links, jbrowse, fasta_compute_length, collapse_dataset, random_lines1, bedtools_sortbed, lastz_wrapper_2, addValue, circos, join1, Filter1, bedtools_intersectbed, bedtools_complementbed, upload1, tp_sed_tool, tp_cat, datamash_ops, tp_sort_header_tool, circos_interval_to_tiles, tp_grep_tool | -- | - | 1 | -2.0 | -5828 | -11935 | -3.033333 | -0 | -
- | Assembly | -Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) | -https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html | -Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance | -De-novo assembly, Sequence composition calculation, Genome assembly, Sequencing error detection, Visualisation, Sequencing quality control, Mapping assembly, Sequence assembly visualisation, Sequence assembly validation, Cross-assembly, Box-Whisker plot plotting, Scatter plot plotting, Filtering, Read mapping, Statistical calculation, Sequence alignment, Sequence contamination filtering | -2021-03-24 | -2024-03-13 | -35 | -True | -False | -False | -True | -flye, nanoplot, bandage_image, polypolish, upload1, quast, porechop, CONVERTER_bz2_to_uncompressed, bwa_mem2, filtlong, fastqc, fastp | -UseGalaxy.eu | -UseGalaxy.cz | -2 | -4.0 | -6353 | -9777 | -3.416667 | -0 | -
- | Genome Annotation | -Bacterial Genome Annotation | -https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html | -Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements | -Structural variation detection, Genome assembly, Nucleic acid feature detection, Protein feature detection, Scaffolding, Multilocus sequence typing, Sequence motif recognition, Genome visualisation, Genome annotation | -2024-02-01 | -2024-03-13 | -8 | -True | -False | -False | -True | -tp_tail_tool, upload1, bakta, isescan, Grouping1, tp_replace_in_column, tbl2gff3, plasmidfinder, integron_finder, jbrowse | -Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr | -- | 1 | -1.0 | -1237 | -1630 | -2.483333 | -0 | -
- | Genome Annotation | -Identification of AMR genes in an assembled bacterial genome | -https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html | -Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance | -Genome annotation, Genome visualisation, Read mapping | -2024-01-23 | -2024-03-13 | -9 | -True | -False | -False | -True | -upload1, staramr_search, bakta, Grep1, bowtie2, tbl2gff3, jbrowse | -UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr | -Galaxy@AuBi | -0 | -- | 726 | -1061 | -3.066667 | -0 | -
- | Genome Annotation | -Refining Genome Annotations with Apollo (prokaryotes) | -https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html | -Genomics, Microbiology, Gene and protein families, Sequence analysis | -Genome visualisation | -2021-06-04 | -2024-05-29 | -40 | -True | -True | -True | -True | -iframe, create_or_update, list_organism, create_account, jbrowse | -- | UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no | -5 | -4.6 | -1757138 | -4755340 | -5.016667 | -0 | -
- | Microbiome | -Analyses of metagenomics data - The global picture | -https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html | -Metagenomics, Microbial ecology, Taxonomy, Sequence analysis | -Sequence read processing, Sequencing quality control, Visualisation, Taxonomic classification, Phylogenetic analysis, DNA barcoding, Sequence clustering | -2017-06-22 | -2024-03-14 | -4 | -True | -False | -False | -True | -mothur_summary_seqs, mothur_classify_seqs, humann2_regroup_table, krona-text, mothur_pre_cluster, mothur_align_seqs, mothur_make_group, mothur_unique_seqs, humann2_renorm_table, metaphlan2, metaphlan2krona, mothur_merge_files, mothur_make_biom, mothur_make_shared, mothur_screen_seqs, mothur_count_seqs, mothur_cluster_split, mothur_classify_otu, mothur_filter_seqs, taxonomy_krona_chart, humann2 | -- | UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au | -16 | -4.0625 | -2225 | -2984 | -2.650000 | -0 | -
- | Microbiome | -Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition | -https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html | -Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis | -Phylogenetic tree reconstruction, Sequence composition calculation, Base-calling, Genome assembly, Phylogenetic tree generation (from molecular sequences), Validation, Visualisation, Sequence assembly visualisation, Multilocus sequence typing, Scatter plot plotting, Statistical calculation, Data handling, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Pairwise sequence alignment, Sequence contamination filtering, De-novo assembly, Sequence alignment analysis, Variant calling, Mapping, Sequencing quality control, Phylogenetic tree generation, Mapping assembly, Box-Whisker plot plotting, Cross-assembly, Taxonomic classification, Antimicrobial resistance prediction, Multiple sequence alignment, Sequence assembly, Aggregation, Phylogenetic tree analysis | -2023-01-26 | -2024-06-19 | -18 | -True | -False | -False | -True | -nanoplot, bandage_image, Cut1, CONVERTER_gz_to_uncompressed, bcftools_consensus, samtools_fastx, Grouping1, tp_replace_in_column, Grep1, __BUILD_LIST__, tp_find_and_replace, regex1, clustalw, fastp, tp_sorted_uniq, collection_element_identifiers, Paste1, flye, Add_a_column1, medaka_consensus_pipeline, Count1, minimap2, table_compute, tp_split_on_column, bamtools_split_mapped, clair3, kraken2, collapse_dataset, __FILTER_EMPTY_DATASETS__, compose_text_param, samtools_depth, snpSift_extractFields, regexColumn1, fastqc, abricate, newick_display, krakentools_extract_kraken_reads, bcftools_norm, barchart_gnuplot, Remove beginning1, samtools_coverage, split_file_to_collection, porechop, tp_multijoin_tool, mlst, tp_head_tool, multiqc, collection_column_join, fasta_merge_files_and_filter_unique_sequences, param_value_from_file, add_line_to_file, krakentools_kreport2krona, bedtools_getfastabed, fasttree, tab2fasta, ggplot2_heatmap, snpSift_filter, __FILTER_FAILED_DATASETS__, taxonomy_krona_chart, fasta2tab, tp_cut_tool | -UseGalaxy.eu | -- | 1 | -5.0 | -1259 | -1884 | -2.800000 | -0 | -
- | Microbiome | -Taxonomic Profiling and Visualization of Metagenomic Data | -https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html | -Metagenomics, Microbial ecology, Taxonomy, Sequence analysis | -Taxonomic classification, Aggregation, Nucleic acid sequence analysis, Statistical calculation, Visualisation, Phylogenetic tree analysis | -2023-05-03 | -2024-05-29 | -4 | -True | -False | -False | -True | -interactive_tool_pavian, interactive_tool_phinch, est_abundance, kraken2, metaphlan, kraken_biom, taxonomy_krona_chart, __UNZIP_COLLECTION__, krakentools_kreport2krona | -UseGalaxy.eu | -UseGalaxy.org.au | -3 | -4.333333 | -2673 | -3680 | -1.900000 | -0 | -
- | Microbiome | -Assembly of metagenomic sequencing data | -https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html | -Metagenomics, Sequence assembly | -Sequence composition calculation, Genome assembly, Visualisation, Primer removal, Sequence assembly visualisation, Sequence file editing, Read mapping, Statistical calculation, Data handling, Sequence contamination filtering, Local alignment, Sequence alignment analysis, Variant calling, Sequencing quality control, Read pre-processing, Sequence assembly validation, Formatting, Sequence trimming | -2022-12-05 | -2024-05-29 | -4 | -True | -False | -False | -True | -filter_tabular, bandage_image, metaspades, megahit, quast, cutadapt, tp_cat, ngsutils_bam_filter, megahit_contig2fastg, random_lines1, bamtools, bowtie2, bandage_info, collection_column_join, coverm_contig, seqtk_subseq, fastqc, bg_uniq | -- | UseGalaxy.cz, UseGalaxy.eu | -0 | -- | 1100 | -1543 | -2.600000 | -0 | -
- | Microbiome | -Antibiotic resistance detection | -https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html | -Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial Resistance | -De-novo assembly, Genome assembly, Mapping assembly, Sequence assembly visualisation, Box-Whisker plot plotting, Scatter plot plotting, Aggregation, Sequence analysis, Pairwise sequence alignment | -2019-06-25 | -2024-05-29 | -4 | -True | -False | -False | -True | -nanoplot, bandage_image, racon, staramr_search, PlasFlow, gfa_to_fa, unicycler, miniasm, minimap2 | -UseGalaxy.eu | -UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au | -10 | -5.0 | -902 | -1419 | -4.050000 | -0 | -
- | Microbiome | -16S Microbial analysis with Nanopore data | -https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html | -Microbial ecology, Taxonomy, Sequence analysis | -Taxonomic classification, Sequence composition calculation, Statistical calculation, Validation, Sequencing quality control, Visualisation, Sequence contamination filtering | -2020-11-24 | -2024-03-21 | -4 | -True | -False | -False | -True | -tp_replace_in_line, kraken2, Remove beginning1, porechop, multiqc, datamash_reverse, taxonomy_krona_chart, fastqc, fastp | -UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au | -GalaxyTrakr, UseGalaxy.cz | -13 | -4.692308 | -1835 | -2617 | -2.900000 | -0 | -
- | Microbiome | -Metatranscriptomics analysis using microbiome RNA-seq data | -https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html | -Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis | -Sequence composition calculation, Phylogenetic tree visualisation, Validation, Phylogenetic inference, Primer removal, Visualisation, Species frequency estimation, Statistical calculation, Phylogenetic analysis, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control, Read pre-processing, Phylogenetic tree editing, Taxonomic classification, Conversion, Nucleic acid sequence analysis, Phylogenetic tree analysis, Sequence trimming | -2019-11-21 | -2024-05-29 | -4 | -True | -True | -False | -True | -graphlan_annotate, Cut1, humann_split_stratified_table, bg_sortmerna, Grep1, tp_find_and_replace, graphlan, humann_renorm_table, humann, metaphlan, humann_rename_table, fastqc, multiqc, combine_metaphlan2_humann2, fastq_paired_end_interlacer, cutadapt, export2graphlan, humann_regroup_table, taxonomy_krona_chart, humann_unpack_pathways | -UseGalaxy.org (Main) | -UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au | -6 | -4.5 | -1986067 | -5535600 | -4.300000 | -0 | -
- | Microbiome | -Metatranscriptomics analysis using microbiome RNA-seq data (short) | -https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html | -Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis | -Sequence composition calculation, Phylogenetic tree visualisation, Validation, Phylogenetic inference, Primer removal, Visualisation, Species frequency estimation, Statistical calculation, Phylogenetic analysis, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control, Read pre-processing, Phylogenetic tree editing, Taxonomic classification, Conversion, Nucleic acid sequence analysis, Phylogenetic tree analysis, Sequence trimming | -2020-02-13 | -2024-05-29 | -4 | -True | -False | -False | -True | -graphlan_annotate, Cut1, humann_split_stratified_table, bg_sortmerna, Grep1, tp_find_and_replace, graphlan, humann_renorm_table, humann, metaphlan, humann_rename_table, fastqc, multiqc, combine_metaphlan2_humann2, fastq_paired_end_interlacer, cutadapt, export2graphlan, humann_regroup_table, taxonomy_krona_chart, humann_unpack_pathways | -UseGalaxy.org (Main) | -UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au | -1 | -5.0 | -184 | -236 | -2.000000 | -0 | -
- | Microbiome | -Identification of the micro-organisms in a beer using Nanopore sequencing | -https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html | -Metagenomics, Microbial ecology, Taxonomy, Sequence analysis | -Taxonomic classification, Sequence composition calculation, Aggregation, Statistical calculation, Sequencing quality control, Visualisation, Sequence contamination filtering | -2022-09-29 | -2024-05-29 | -4 | -True | -False | -False | -True | -kraken2, porechop, taxonomy_krona_chart, fastqc, fastp, Filter1, krakentools_kreport2krona | -GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au | -UseGalaxy.cz | -3 | -4.666667 | -969 | -1570 | -3.000000 | -0 | -
- | Microbiome | -Building an amplicon sequence variant (ASV) table from 16S data using DADA2 | -https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html | -Microbial ecology, Taxonomy, Sequence analysis | -Variant calling, DNA barcoding, Deposition, Visualisation, Analysis | -2024-06-05 | -2024-06-17 | -9 | -True | -False | -False | -True | -tp_replace_in_line, dada2_filterAndTrim, dada2_plotQualityProfile, Grouping1, tp_replace_in_column, cat1, interactive_tool_phyloseq, collection_element_identifiers, Add_a_column1, dada2_mergePairs, dada2_seqCounts, __UNZIP_COLLECTION__, __SORTLIST__, dada2_dada, dada2_makeSequenceTable, phyloseq_from_dada2, tp_head_tool, dada2_removeBimeraDenovo, dada2_learnErrors, dada2_assignTaxonomyAddspecies | -UseGalaxy.eu, UseGalaxy.fr | -- | 0 | -- | 104 | -129 | -1.483333 | -0 | -
- | Microbiome | -QIIME 2 Cancer Microbiome Intervention | -https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html | -Microbial ecology, Taxonomy, Sequence analysis | -- | 2024-02-12 | -2024-03-14 | -6 | -external | -False | -False | -False | -- | - | UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr | -1 | -5.0 | -83 | -152 | -1.233333 | -0 | -
- | Microbiome | -Binning of metagenomic sequencing data | -https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html | -Metagenomics, Sequence assembly | -Sequence composition calculation, Genome assembly, Statistical calculation, Validation, Sequencing quality control, Sequence assembly validation | -2023-12-05 | -2024-03-14 | -4 | -True | -False | -False | -False | -checkm_lineage_wf, megahit | -GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr | -- | 0 | -- | 1134 | -1367 | -1.516667 | -0 | -
- | Microbiome | -QIIME 2 Moving Pictures | -https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html | -Microbial ecology, Taxonomy, Sequence analysis | -- | 2024-03-14 | -2024-03-14 | -2 | -external | -False | -False | -False | -- | - | UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr | -1 | -5.0 | -72 | -94 | -3.416667 | -0 | -
- | Microbiome | -16S Microbial Analysis with mothur (short) | -https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html | -Microbial ecology, Taxonomy, Sequence analysis | -Phylogenetic tree reconstruction, Sequence read processing, Sequencing quality control, Visualisation, Phylogenetic tree generation, Taxonomic classification, Phylogenetic analysis, DNA barcoding, Sequence clustering, Phylogenetic tree analysis | -2019-05-13 | -2024-05-31 | -7 | -True | -False | -False | -True | -mothur_summary_seqs, mothur_classify_seqs, mothur_pre_cluster, mothur_rarefaction_single, mothur_remove_lineage, mothur_unique_seqs, collapse_dataset, XY_Plot_1, newick_display, mothur_sub_sample, mothur_summary_single, mothur_venn, mothur_make_shared, mothur_heatmap_sim, mothur_dist_shared, mothur_screen_seqs, mothur_count_seqs, mothur_cluster_split, mothur_remove_seqs, mothur_classify_otu, mothur_filter_seqs, mothur_remove_groups, mothur_cluster, mothur_count_groups, mothur_dist_seqs, mothur_chimera_vsearch, mothur_tree_shared | -UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au | -UseGalaxy.cz, UseGalaxy.fr | -9 | -4.666667 | -1485 | -2824 | -6.050000 | -0 | -
- | Microbiome | -16S Microbial Analysis with mothur (extended) | -https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html | -Microbial ecology, Taxonomy, Sequence analysis | -Phylogenetic tree reconstruction, Sequence read processing, Sequencing quality control, Visualisation, Phylogenetic tree generation, Taxonomic classification, Phylogenetic analysis, DNA barcoding, Sequence clustering, Phylogenetic tree analysis | -2017-02-12 | -2024-03-14 | -4 | -True | -False | -False | -True | -mothur_make_contigs, mothur_seq_error, mothur_summary_seqs, mothur_classify_seqs, mothur_pre_cluster, mothur_align_seqs, mothur_rarefaction_single, mothur_remove_lineage, mothur_unique_seqs, mothur_taxonomy_to_krona, XY_Plot_1, newick_display, mothur_sub_sample, mothur_summary_single, mothur_make_biom, mothur_venn, mothur_make_shared, mothur_heatmap_sim, mothur_dist_shared, mothur_screen_seqs, mothur_get_groups, mothur_count_seqs, mothur_cluster_split, mothur_remove_seqs, mothur_classify_otu, mothur_filter_seqs, mothur_remove_groups, mothur_cluster, taxonomy_krona_chart, mothur_count_groups, mothur_dist_seqs, mothur_chimera_vsearch, mothur_tree_shared | -UseGalaxy.eu | -UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au | -44 | -4.613636 | -3646 | -5683 | -3.133333 | -0 | -
- | Variant Analysis | -M. tuberculosis Variant Analysis | -https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html | -Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease | -Local alignment, Sequence composition calculation, Sequence alignment analysis, Global alignment, Variant calling, Validation, Sequencing quality control, Phylogenetic tree generation, Antimicrobial resistance prediction, Taxonomic classification, Genome visualisation, Statistical calculation, Sequence alignment, Sequence analysis, Phylogenetic tree visualisation, Sequence contamination filtering | -2020-07-25 | -2024-06-12 | -75 | -True | -False | -False | -True | -tb_variant_filter, bcftools_consensus, jvarkit_wgscoverageplotter, fastp, jbrowse, snippy, kraken2, EMBOSS:%20seqret84, qualimap_bamqc, fastqc, tb_profiler_profile, EMBOSS: seqret84, mosdepth, tbvcfreport, __FLATTEN__, multiqc, upload1, tp_sed_tool, samtools_stats, tp_awk_tool | -- | - | 25 | -4.64 | -5340 | -8587 | -2.966667 | -0 | -
- | Genome Annotation | -Identification of AMR genes in an assembled bacterial genome | -https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html | -Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance | -Genome annotation, Genome visualisation, Read mapping | -2024-01-23 | -2024-03-13 | -9 | -True | -False | -False | -True | -upload1, staramr_search, bakta, Grep1, bowtie2, tbl2gff3, jbrowse | -UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr | -Galaxy@AuBi | -0 | -- | 726 | -1061 | -3.066667 | -0 | -
- | Evolution | -Tree thinking for tuberculosis evolution and epidemiology | -https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html | -Genomics, Microbiology, Phylogeny, Infectious disease | -Sequence analysis, Phylogenetic tree analysis | -2022-03-16 | -2023-02-15 | -19 | -True | -False | -False | -True | -raxml, interactive_tool_rstudio, upload1 | -UseGalaxy.eu | -UseGalaxy.fr, UseGalaxy.org (Main) | -6 | -4.333333 | -1211 | -1857 | -2.266667 | -0 | -
- | Evolution | -Identifying tuberculosis transmission links: from SNPs to transmission clusters | -https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html | -Genomics, Microbiology, Infectious disease, DNA polymorphism | -Antimicrobial resistance prediction, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling | -2022-03-16 | -2024-03-12 | -15 | -True | -False | -False | -True | -snippy, tb_variant_filter, tp_replace_in_line, trimmomatic, bcftools_consensus, snp_sites, tp_sed_tool, addName, tp_cat, upload1, collapse_dataset, Grep1, __MERGE_COLLECTION__, tp_easyjoin_tool, tb_profiler_profile, samtools_view, tp_grep_tool, snp_dists | -UseGalaxy.eu | -UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) | -7 | -4.0 | -1377 | -2211 | -3.183333 | -0 | -
- | Proteomics | -metaQuantome 3: Taxonomy | -https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html | -Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy | -Statistical inference, Quantification, Functional clustering, Visualisation, Filtering, Principal component visualisation, Indexing, Query and retrieval, Differential protein expression analysis, Heat map generation | -2020-10-29 | -2024-03-14 | -36 | -True | -False | -False | -True | -metaquantome_filter, metaquantome_expand, metaquantome_sample, metaquantome_viz, metaquantome_db, metaquantome_stat | -UseGalaxy.eu | -UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au | -0 | -- | 357 | -487 | -2.733333 | -0 | -
- | Proteomics | -Metaproteomics tutorial | -https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html | -Proteomics, Proteogenomics, Biodiversity, Taxonomy | -Prediction and recognition, Visualisation | -2017-06-28 | -2024-05-29 | -57 | -True | -False | -False | -True | -search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept | -UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au | -UseGalaxy.cz | -1 | -5.0 | -2198 | -3676 | -2.683333 | -0 | -
- | Proteomics | -metaQuantome 1: Data creation | -https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html | -Proteomics, Proteogenomics, Biodiversity, Taxonomy | -Prediction and recognition, Formatting, Visualisation, Label-free quantification, Filtering | -2020-10-16 | -2024-03-14 | -90 | -True | -False | -False | -True | -flashlfq, Cut1, tp_replace_in_line, Remove beginning1, tp_replace_in_column, Grep1, unipept, peptide_shaker, regex1, msconvert, query_tabular, Filter1, search_gui | -UseGalaxy.eu | -UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au | -0 | -- | 757 | -1325 | -3.866667 | -0 | -
- | Proteomics | -metaQuantome 2: Function | -https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html | -Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics | -Statistical inference, Quantification, Functional clustering, Visualisation, Filtering, Principal component visualisation, Indexing, Query and retrieval, Differential protein expression analysis, Heat map generation | -2020-10-29 | -2024-03-14 | -38 | -True | -False | -False | -True | -metaquantome_filter, metaquantome_expand, metaquantome_sample, metaquantome_viz, metaquantome_db, metaquantome_stat | -UseGalaxy.eu | -UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au | -0 | -- | 337 | -489 | -3.866667 | -0 | -
- | Variant Analysis | -Calling variants in non-diploid systems | -https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html | -Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation | -Sequence composition calculation, Sequence alignment analysis, Generation, Sequence alignment, Variant calling, Genome indexing, Sequencing quality control, Formatting, Read mapping, Statistical calculation, Data handling | -2017-02-16 | -2024-03-14 | -39 | -True | -False | -False | -True | -picard_MergeSamFiles, fastqc, Cut1, picard_MarkDuplicates, freebayes, vcf2tsv, bamFilter, bwa_mem, bamleftalign, vcffilter2 | -UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) | -UseGalaxy.cz, UseGalaxy.org.au | -3 | -2.333333 | -6849 | -13178 | -2.050000 | -0 | -
- | Variant Analysis | -M. tuberculosis Variant Analysis | -https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html | -Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease | -Local alignment, Sequence composition calculation, Sequence alignment analysis, Global alignment, Variant calling, Validation, Sequencing quality control, Phylogenetic tree generation, Antimicrobial resistance prediction, Taxonomic classification, Genome visualisation, Statistical calculation, Sequence alignment, Sequence analysis, Phylogenetic tree visualisation, Sequence contamination filtering | -2020-07-25 | -2024-06-12 | -75 | -True | -False | -False | -True | -tb_variant_filter, bcftools_consensus, jvarkit_wgscoverageplotter, fastp, jbrowse, snippy, kraken2, EMBOSS:%20seqret84, qualimap_bamqc, fastqc, tb_profiler_profile, EMBOSS: seqret84, mosdepth, tbvcfreport, __FLATTEN__, multiqc, upload1, tp_sed_tool, samtools_stats, tp_awk_tool | -- | - | 25 | -4.64 | -5340 | -8587 | -2.966667 | -0 | -
- | Variant Analysis | -Microbial Variant Calling | -https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html | -Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation | -Genome visualisation, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling | -2018-02-26 | -2024-03-14 | -36 | -True | -False | -False | -True | -snippy, jbrowse | -UseGalaxy.eu, UseGalaxy.org (Main) | -GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au | -12 | -4.416667 | -11631 | -19648 | -1.983333 | -0 | -
Expand | -Galaxy wrapper id | -Galaxy tool ids | -Description | -bio.tool id | -bio.tool ids | -biii | -bio.tool name | -bio.tool description | -EDAM operation | -EDAM topic | -Status | -Source | -ToolShed categories | -ToolShed id | -Galaxy wrapper owner | -Galaxy wrapper source | -Galaxy wrapper parsed folder | -Galaxy wrapper version | -Conda id | -Conda version | -EDAM operation (no superclasses) | -EDAM topic (no superclasses) | -Available on UseGalaxy.org (Main) | -Available on UseGalaxy.org.au | -Available on UseGalaxy.eu | -Available on UseGalaxy.fr | -Tools available on UseGalaxy.org (Main) | -Tools available on UseGalaxy.org.au | -Tools available on UseGalaxy.eu | -Tools available on UseGalaxy.fr | -Tools available on ANASTASIA | -Tools available on APOSTL | -Tools available on ARGs-OAP | -Tools available on BF2I-MAP | -Tools available on BioBix | -Tools available on CIRM-CFBP | -Tools available on Center for Phage Technology (CPT) | -Tools available on ChemFlow | -Tools available on Coloc-stats | -Tools available on CorGAT | -Tools available on CropGalaxy | -Tools available on Dintor | -Tools available on FreeBioinfo | -Tools available on GASLINI | -Tools available on Galaxy@AuBi | -Tools available on Galaxy@Pasteur | -Tools available on GalaxyTrakr | -Tools available on Genomic Hyperbrowser | -Tools available on GigaGalaxy | -Tools available on HyPhy HIV NGS Tools | -Tools available on IPK Galaxy Blast Suite | -Tools available on ImmPort Galaxy | -Tools available on InteractoMIX | -Tools available on MISSISSIPPI | -Tools available on Mandoiu Lab | -Tools available on MiModD NacreousMap | -Tools available on Oqtans | -Tools available on Palfinder | -Tools available on PepSimili | -Tools available on PhagePromotor | -Tools available on Protologger | -Tools available on UseGalaxy.be | -Tools available on UseGalaxy.cz | -Tools available on UseGalaxy.no | -No. of tool users (2022-2023) (usegalaxy.eu) | -Total tool usage (usegalaxy.eu) | -Deprecated | -
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- | aegean | -aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval | -AEGeAn toolkit wrappers | -gaeval | -gaeval | -- | GAEVAL | -Gene Annotation EVAluation. | -Sequence annotation | -Sequence analysis, Gene structure | -Up-to-date | -https://github.com/BrendelGroup/AEGeAn | -Transcriptomics, Sequence Analysis | -aegean | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean | -0.16.0 | -aegean | -0.16.0 | -Sequence annotation | -Sequence analysis, Gene structure | -1 | -4 | -4 | -4 | -1 | -4 | -4 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -47 | -168 | -- |
- | anndata | -anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom | -Import, Export, Inspect and Manipulate Anndata and Loom objects | -- | - | - | - | - | - | - | To update | -https://anndata.readthedocs.io | -Transcriptomics, Sequence Analysis | -anndata | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata | -0.10.3 | -anndata | -0.6.22.post1 | -- | - | 5 | -4 | -5 | -0 | -5 | -4 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -625 | -35620 | -- |
- | arriba | -arriba, arriba_draw_fusions, arriba_get_filters | -Arriba detects fusion genes in RNA-Seq data after running RNA-STAR | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/suhrig/arriba | -Sequence Analysis, Transcriptomics | -arriba | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba | -2.4.0 | -arriba | -2.4.0 | -- | - | 0 | -3 | -3 | -0 | -0 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -0 | -38 | -3528 | -- |
- | askor | -askor_de | -AskoR links EdgeR and AskOmics | -- | - | - | - | - | - | - | To update | -https://github.com/askomics/askoR | -Transcriptomics | -askor_de | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/askor | -https://github.com/genouest/galaxy-tools/tree/master/tools/askor | -0.2 | -bioconductor-limma | -3.58.1 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | bamparse | -bamparse | -Generates hit count lists from bam alignments. | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -RNA, Transcriptomics | -bamparse | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse | -https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse | -4.1.1 | -pysam | -0.22.1 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | baredsc | -baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d | -baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. | -baredsc | -baredsc | -- | baredSC | -The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. | -Data retrieval, Expression correlation analysis, Differential gene expression profiling | -RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability | -Up-to-date | -https://github.com/lldelisle/baredSC | -Transcriptomics, Visualization | -baredsc | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc | -1.1.3 | -baredsc | -1.1.3 | -Data retrieval, Expression correlation analysis, Differential gene expression profiling | -RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability | -4 | -0 | -4 | -0 | -4 | -0 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -0 | -71 | -- |
- | bctools | -bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events | -bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/dmaticzka/bctools | -Sequence Analysis, Transcriptomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools | -0.2.2 | -bctools | -0.2.2 | -- | - | 0 | -0 | -7 | -0 | -0 | -0 | -7 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -7 | -7 | -87 | -2895 | -- |
- | brew3r_r | -brew3r_r | -Extend 3' end of a GTF using another GTF as a template | -- | - | - | - | - | - | - | To update | -https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html | -Transcriptomics, RNA | -brew3r_r | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r | -1.0.2 | -- | - | - | - | 1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | cell-types-analysis | -ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals | -Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis | -- | - | - | - | - | - | - | To update | -- | Transcriptomics, RNA, Statistics | -suite_cell_types_analysis | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis | -1.1.1 | -cell-types-analysis | -0.1.11 | -- | - | 0 | -0 | -6 | -0 | -0 | -0 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -6 | -- |
- | cemitool | -cemitool | -Gene co-expression network analysis tool | -cemitool | -cemitool | -- | CEMiTool | -It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. | -Enrichment analysis, Pathway or network analysis | -Gene expression, Transcriptomics, Microarray experiment | -To update | -https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html | -Transcriptomics, RNA, Statistics | -cemitool | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool | -1.18.1 | -bioconductor-cemitool | -1.26.0 | -Enrichment analysis, Pathway or network analysis | -Transcriptomics, Microarray experiment | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -9 | -98 | -- |
- | cherri | -cherri_eval, cherri_train | -Computational Help Evaluating RNA-RNA interactions | -cherri | -cherri | -- | cherri | -CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. | -- | Molecular interactions, pathways and networks, Structure analysis, Machine learning | -To update | -https://github.com/BackofenLab/Cherri | -Transcriptomics, RNA | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri | -0.7 | -cherri | -0.8 | -- | Molecular interactions, pathways and networks, Structure analysis, Machine learning | -0 | -0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -1 | -207 | -- |
- | chira | -chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify | -Chimeric Read Annotator for RNA-RNA interactome data | -chira | -chira | -- | ChiRA | -ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. | -- | RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA | -Up-to-date | -https://github.com/pavanvidem/chira | -RNA, Transcriptomics, Sequence Analysis | -chira | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira | -1.4.3 | -chira | -1.4.3 | -- | Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA | -5 | -0 | -5 | -0 | -5 | -0 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -97 | -6418 | -- |
- | cite_seq_count | -cite_seq_count | -Count CMO/HTO | -CITE-seq-Count | -CITE-seq-Count | -- | CITE-seq-Count | -Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. | -RNA-Seq quantification | -Transcriptomics, Immunoproteins and antigens | -Up-to-date | -https://github.com/Hoohm/CITE-seq-Count | -Transcriptomics | -cite_seq_count | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count | -1.4.4 | -cite-seq-count | -1.4.4 | -RNA-Seq quantification | -Transcriptomics, Immunoproteins and antigens | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -18 | -- |
- | cosg | -cosg | -Marker gene identification for single-cell sequencing data using COSG. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/genecell/COSG | -Transcriptomics, Sequence Analysis | -cosg | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg | -1.0.1 | -cosg | -1.0.1 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | cpat | -cpat | -Coding-potential assessment tool using an alignment-free logistic regression model. | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/liguowang/cpat | -Transcriptomics | -cpat | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/cpat | -https://github.com/bgruening/galaxytools/tree/master/tools/cpat | -3.0.5 | -cpat | -3.0.5 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -21 | -134 | -- |
- | cpm_tpm_rpk | -cpm_tpm_rpk | -Generate CPM,TPM or RPK from raw counts | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Transcriptomics | -cpm_tpm_rpk | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk | -https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk | -0.5.2 | -r-optparse | -1.3.2 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | crosscontamination_barcode_filter | -crosscontamination_barcode_filter | -Barcode contamination discovery tool | -- | - | - | - | - | - | - | To update | -- | Transcriptomics, Visualization | -crosscontamination_barcode_filter | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter | -0.3 | -r-ggplot2 | -2.2.1 | -- | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -17 | -347 | -- |
- | cuffcompare | -cuffcompare | -Galaxy wrappers for the Cuffcompare tool. | -- | - | - | - | - | - | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cuffcompare | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare | -2.2.1 | -cufflinks | -2.2.1 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -65 | -1130 | -- |
- | cuffdiff | -cuffdiff | -Galaxy wrappers for the Cuffdiff tool. | -- | - | - | - | - | - | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cuffdiff | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff | -2.2.1 | -cufflinks | -2.2.1 | -- | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -228 | -5831 | -- |
- | cufflinks | -cufflinks | -Galaxy wrappers for the Cufflinks tool. | -- | - | - | - | - | - | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cufflinks | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks | -2.2.1 | -cufflinks | -2.2.1 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -319 | -32218 | -- |
- | cuffmerge | -cuffmerge | -Galaxy wrappers for the Cuffmerge tool. | -- | - | - | - | - | - | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cuffmerge | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge | -2.2.1 | -cufflinks | -2.2.1 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -122 | -3292 | -- |
- | cuffnorm | -cuffnorm | -The Cuffnorm tool | -- | - | - | - | - | - | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cuffnorm | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm | -2.2.1 | -cufflinks | -2.2.1 | -- | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -27 | -660 | -- |
- | cuffquant | -cuffquant | -The Cuffquant tool | -- | - | - | - | - | - | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cuffquant | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant | -2.2.1 | -cufflinks | -2.2.1 | -- | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -18 | -688 | -- |
- | data-hca | -hca_matrix_downloader | -Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects | -- | - | - | - | - | - | - | To update | -- | Transcriptomics, Sequence Analysis | -suite_human_cell_atlas_tools | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca | -v0.0.4+galaxy0 | -hca-matrix-downloader | -0.0.4 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -34 | -439 | -- |
- | data-scxa | -retrieve_scxa | -Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home | -- | - | - | - | - | - | - | To update | -- | Transcriptomics, Sequence Analysis | -suite_ebi_expression_atlas | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa | -v0.0.2+galaxy2 | -wget | -- | - | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -99 | -799 | -- |
- | decoupler | -score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk | -decoupler - Ensemble of methods to infer biological activities | -- | - | - | - | - | - | - | To update | -https://decoupler-py.readthedocs.io/en/latest/ | -Transcriptomics | -suite_decoupler | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler | -1.4.0+galaxy3 | -decoupler | -1.5.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -- |
- | deg_annotate | -deg_annotate | -Annotate DESeq2/DEXSeq output tables | -- | - | - | - | - | - | - | To update | -- | Transcriptomics | -deg_annotate | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate | -1.1.0 | -bedtools | -2.31.1 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1774 | -19910 | -- |
- | deseq2 | -deseq2 | -Differential gene expression analysis based on the negative binomial distribution | -DESeq2 | -DESeq2 | -- | DESeq2 | -R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. | -Differential gene expression analysis, RNA-Seq analysis | -RNA-Seq | -To update | -https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html | -Transcriptomics, RNA, Statistics | -deseq2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 | -2.11.40.8 | -bioconductor-deseq2 | -1.42.0 | -Differential gene expression analysis, RNA-Seq analysis | -RNA-Seq | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -1 | -4990 | -95752 | -- |
- | deseq2_normalization | -deseq2_normalization | -Normalizes gene hitlists | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -RNA, Transcriptomics, Sequence Analysis, Statistics | -deseq2_normalization | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization | -https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization | -1.40.2+galaxy0 | -bioconductor-deseq2 | -1.42.0 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | dexseq | -dexseq, dexseq_count, plotdexseq | -Inference of differential exon usage in RNA-Seq | -dexseq | -dexseq | -- | DEXSeq | -The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. | -Enrichment analysis, Exonic splicing enhancer prediction | -RNA-Seq | -Up-to-date | -https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html | -Transcriptomics, RNA, Statistics | -dexseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq | -1.48.0 | -bioconductor-dexseq | -1.48.0 | -Enrichment analysis, Exonic splicing enhancer prediction | -RNA-Seq | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -3 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -218 | -16064 | -- |
- | dropletutils | -dropletutils_empty_drops, dropletutils_read_10x | -De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 | -- | - | - | - | - | - | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_dropletutils | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils | -1.0.4 | -dropletutils-scripts | -0.0.5 | -- | - | 2 | -0 | -2 | -0 | -2 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -201 | -1599 | -- |
- | dropletutils | -dropletutils | -DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data | -dropletutils | -dropletutils | -- | DropletUtils | -Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. | -Loading, Community profiling | -Gene expression, RNA-seq, Sequencing, Transcriptomics | -To update | -https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html | -Transcriptomics, Sequence Analysis | -dropletutils | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils | -1.10.0 | -bioconductor-dropletutils | -1.22.0 | -- | Sequencing, Transcriptomics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -126 | -3934 | -- |
- | edger | -edger | -Perform RNA-Seq differential expression analysis using edgeR pipeline | -edger | -edger | -- | edgeR | -Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. | -Differential gene expression analysis | -Genetics, RNA-Seq, ChIP-seq | -To update | -http://bioconductor.org/packages/release/bioc/html/edgeR.html | -Transcriptomics, RNA, Statistics | -edger | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger | -3.36.0 | -bioconductor-edger | -4.0.16 | -Differential gene expression analysis | -Genetics, RNA-Seq, ChIP-seq | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -945 | -18117 | -- |
- | egsea | -egsea | -This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing | -egsea | -egsea | -- | EGSEA | -This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. | -Gene set testing | -Systems biology | -To update | -https://bioconductor.org/packages/release/bioc/html/EGSEA.html | -Transcriptomics, RNA, Statistics | -egsea | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea | -1.20.0 | -bioconductor-egsea | -1.28.0 | -Gene set testing | -Systems biology | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -177 | -2524 | -- |
- | fastq_provider | -fastq_provider | -Retrieval and download of FASTQ files from ENA and other repositories such as HCA. | -- | - | - | - | - | - | - | To update | -https://github.com/ebi-gene-expression-group/atlas-fastq-provider | -Data Source, RNA, Transcriptomics | -atlas_fastq_provider | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider | -0.4.4 | -atlas-fastq-provider | -0.4.7 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | fastq_utils | -fastq_filter_n, fastq_trim_poly_at | -Set of tools for handling fastq files | -- | - | - | - | - | - | - | To update | -https://github.com/nunofonseca/fastq_utils | -Transcriptomics, RNA | -fastq_utils | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils | -0.25.1+galaxy0 | -fastq_utils | -0.25.2 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | featurecounts | -featurecounts | -featureCounts counts the number of reads aligned to defined masked regions in a reference genome | -featurecounts | -featurecounts | -- | FeatureCounts | -featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. | -Read summarisation, RNA-Seq quantification | -RNA-Seq | -To update | -http://bioinf.wehi.edu.au/featureCounts | -RNA, Transcriptomics, Sequence Analysis | -featurecounts | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts | -2.0.3 | -subread | -2.0.6 | -Read summarisation, RNA-Seq quantification | -RNA-Seq | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -1 | -1 | -4679 | -696399 | -- |
- | fgsea | -fgsea | -Perform gene set testing using fgsea | -fgsea | -fgsea | -- | fgsea | -The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. | -Gene-set enrichment analysis | -Genetics | -To update | -https://bioconductor.org/packages/release/bioc/html/fgsea.html | -Visualization, Transcriptomics, Statistics | -fgsea | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea | -1.8.0+galaxy1 | -bioconductor-fgsea | -1.28.0 | -Gene-set enrichment analysis | -Genetics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -307 | -5240 | -- |
- | garnett | -garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file | -De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 | -- | - | - | - | - | - | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_garnett | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett | -0.2.8 | -garnett-cli | -0.0.5 | -- | - | 0 | -0 | -7 | -0 | -0 | -0 | -7 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -27 | -- |
- | genomic_super_signature | -genomic_super_signature | -Interpretation of RNAseq experiments through robust, efficient comparison to public databases | -genomicsupersignature | -genomicsupersignature | -- | GenomicSuperSignature | -GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. | -Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction | -RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment | -To update | -https://github.com/shbrief/GenomicSuperSignature | -Sequence Analysis, RNA, Transcriptomics | -genomic_super_signature | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature | -1.2.0 | -bioconductor-genomicsupersignature | -1.10.0 | -Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction | -RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -11 | -46 | -- |
- | gffcompare | -gffcompare | -Galaxy wrappers for Geo Pertea's GffCompare package. | -gffcompare | -gffcompare | -- | gffcompare | -Program for comparing, annotating, merging and tracking transcripts in GFF files. | -Sequence annotation | -Nucleic acids, Sequence analysis | -Up-to-date | -https://github.com/gpertea/gffcompare/ | -Transcriptomics | -gffcompare | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare | -0.12.6 | -gffcompare | -0.12.6 | -Sequence annotation | -Nucleic acids, Sequence analysis | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -381 | -3477 | -- |
- | gsc_filter_cells | -filter_cells | -Filter single cell RNAseq data on libray depth and number of detected genes | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_filter_cells | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells | -4.3.1+galaxy0 | -r-optparse | -1.3.2 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | gsc_filter_genes | -filter_genes | -Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_filter_genes | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes | -4.3.1+galaxy0 | -r-optparse | -1.3.2 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | gsc_gene_expression_correlations | -single_cell_gene_expression_correlations | -Compute single-cell paire-wise gene expressions correlations | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_gene_expression_correlations | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations | -4.3.1+galaxy0 | -r-optparse | -1.3.2 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | gsc_high_dimensions_visualisation | -high_dimensions_visualisation | -Generates PCA, t-SNE and HCPC visualisation | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Transcriptomics, Visualization | -gsc_high_dimensions_visualisation | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation | -4.3+galaxy0 | -r-optparse | -1.3.2 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | gsc_mannwhitney_de | -mannwhitney_de | -Perform a mann-whitney differential testing between two sets of gene expression data | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_mannwhitney_de | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de | -4.1.3+galaxy0 | -r-optparse | -1.3.2 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | gsc_scran_normalize | -scran_normalize | -Normalize raw counts using scran | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_scran_normalize | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize | -1.28.1+galaxy0 | -bioconductor-scran | -1.30.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -14 | -78 | -- |
- | gsc_signature_score | -signature_score | -Compute signature scores from single cell RNAseq data | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_signature_score | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score | -2.3.9+galaxy0 | -r-optparse | -1.3.2 | -- | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | heinz | -heinz_bum, heinz, heinz_scoring, heinz_visualization | -An algorithm for identification of the optimal scoring subnetwork. | -heinz | -heinz, bionet | -- | Heinz | -Tool for single-species active module discovery. | -Pathway or network analysis | -Genetics, Gene expression, Molecular interactions, pathways and networks | -To update | -https://github.com/ls-cwi/heinz | -Transcriptomics, Visualization, Statistics | -heinz | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz | -1.0 | -bioconductor-bionet | -1.62.0 | -Pathway or network analysis | -Genetics, Gene expression, Molecular interactions, pathways and networks | -4 | -4 | -4 | -0 | -4 | -4 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -4 | -242 | -1186 | -- |
- | isoformswitchanalyzer | -isoformswitchanalyzer | -Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. | -IsoformSwitchAnalyzeR | -IsoformSwitchAnalyzeR | -- | IsoformSwitchAnalyzeR | -Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. | -Sequence comparison, Sequence analysis | -Computational biology, Gene transcripts | -To update | -https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html | -Transcriptomics, RNA, Statistics | -isoformswitchanalyzer | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer | -1.20.0 | -bioconductor-isoformswitchanalyzer | -2.2.0 | -Sequence comparison, Sequence analysis | -Computational biology, Gene transcripts | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -29 | -822 | -- |
- | kallisto | -kallisto_pseudo, kallisto_quant | -kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. | -kallisto | -kallisto | -- | kallisto | -A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. | -Gene expression profiling | -Transcriptomics, RNA-seq, Gene expression | -To update | -https://pachterlab.github.io/kallisto/ | -Transcriptomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto | -0.48.0 | -kallisto | -0.50.1 | -Gene expression profiling | -Transcriptomics | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -299 | -24155 | -- |
- | limma_voom | -limma_voom | -Perform RNA-Seq differential expression analysis using limma voom pipeline | -limma | -limma | -- | limma | -Data analysis, linear models and differential expression for microarray data. | -RNA-Seq analysis | -Molecular biology, Genetics | -Up-to-date | -http://bioconductor.org/packages/release/bioc/html/limma.html | -Transcriptomics, RNA, Statistics | -limma_voom | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom | -3.58.1 | -bioconductor-limma | -3.58.1 | -RNA-Seq analysis | -Molecular biology, Genetics | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1012 | -20344 | -- |
- | masigpro | -masigpro | -Identify significantly differential expression profiles in time-course microarray experiments | -masigpro | -masigpro | -- | maSigPro | -Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. | -Regression analysis | -Gene expression, Molecular genetics, Microarray experiment, RNA-Seq | -To update | -https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html | -Transcriptomics, RNA, Statistics | -masigpro | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro | -1.49.3 | -coreutils | -8.25 | -Regression analysis | -Gene expression, Microarray experiment, RNA-Seq | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -13 | -576 | -- |
- | mircounts | -mircounts | -Generates miRNA count lists from read alignments to mirBase. | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -RNA, Transcriptomics | -mircounts | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts | -https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts | -1.6 | -tar | -- | - | - | 0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | monocle3 | -monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers | -De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. | -- | - | - | - | - | - | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_monocle3 | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 | -0.1.4 | -monocle3-cli | -0.0.9 | -- | - | 9 | -0 | -9 | -0 | -9 | -0 | -9 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -264 | -3266 | -- |
- | multigsea | -multigsea | -GSEA-based pathway enrichment analysis for multi-omics data | -multiGSEA | -multiGSEA | -- | multiGSEA | -A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. | -Gene-set enrichment analysis, Aggregation, Pathway analysis | -Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules | -Up-to-date | -https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html | -Transcriptomics, Proteomics, Statistics | -multigsea | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea | -1.12.0 | -bioconductor-multigsea | -1.12.0 | -Gene-set enrichment analysis, Aggregation, Pathway analysis | -Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -2 | -53 | -- |
- | music_deconvolution | -music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution | -Multi-subject Single Cell deconvolution (MuSiC) | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/xuranw/MuSiC | -Transcriptomics | -music | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ | -https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution | -0.1.1 | -music-deconvolution | -0.1.1 | -- | - | 5 | -5 | -4 | -0 | -5 | -5 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -240 | -1872 | -- |
- | nugen_nudup | -nugen_nudup | -Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. | -nudup | -nudup | -- | NuDup | -Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. | -Duplication detection | -Sequencing | -Up-to-date | -https://github.com/tecangenomics/nudup | -SAM, Metagenomics, Sequence Analysis, Transcriptomics | -nugen_nudup | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup | -2.3.3 | -nudup | -2.3.3 | -Duplication detection | -Sequencing | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | pathifier | -pathifier | -pathifier | -- | - | - | - | - | - | - | Up-to-date | -https:// | -Transcriptomics, Statistics | -pathifier | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier | -https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier | -1.40.0 | -bioconductor-pathifier | -1.40.0 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -10 | -228 | -- |
- | pizzly | -pizzly | -Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. | -- | - | - | - | - | - | - | To update | -https://github.com/pmelsted/pizzly/ | -Transcriptomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly | -0.37.3.1 | -pizzly | -0.37.3 | -- | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -16 | -208 | -- |
- | psiclass | -psiclass | -PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. | -psiclass | -psiclass | -- | - | - | - | - | Up-to-date | -https://github.com/splicebox/PsiCLASS | -Transcriptomics | -psiclass | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass | -1.0.3 | -psiclass | -1.0.3 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -15 | -- |
- | qualimap | -qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq | -- | qualimap | -qualimap | -- | QualiMap | -Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. | -Sequencing quality control | -Data quality management | -To update | -http://qualimap.bioinfo.cipf.es/ | -Sequence Analysis, Transcriptomics, SAM | -qualimap | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap | -2.2.2d | -qualimap | -2.3 | -Sequencing quality control | -Data quality management | -4 | -4 | -4 | -1 | -4 | -4 | -4 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -4 | -1328 | -664470 | -- |
- | raceid | -raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory | -RaceID3, StemID2, FateID - scRNA analysis | -- | - | - | - | - | - | - | To update | -https://github.com/dgrun/RaceID3_StemID2_package/ | -Transcriptomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid | -0.2.3 | -r-raceid | -0.1.3 | -- | - | 5 | -5 | -5 | -1 | -5 | -5 | -5 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -82 | -4569 | -- |
- | repenrich | -edger-repenrich, repenrich | -Repeat element profiling | -- | - | - | - | - | - | - | To update | -https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich | -Transcriptomics | -repenrich | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich | -https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich | -2.31.1 | -- | - | - | - | 0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | repenrich2 | -edger-repenrich2, repenrich2 | -Repeat element profiling using bowtie2 aligner | -- | - | - | - | - | - | - | To update | -https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 | -Transcriptomics | -repenrich2 | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 | -https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 | -2.31.1 | -- | - | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | rgrnastar | -rna_star, rna_starsolo | -RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper | -star | -star | -- | STAR | -Ultrafast universal RNA-seq data aligner | -Sequence alignment | -RNA-Seq, Transcriptomics | -To update | -https://github.com/alexdobin/STAR | -Next Gen Mappers, Transcriptomics | -rgrnastar | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar | -2.7.11a | -star | -2.7.11b | -Sequence alignment | -RNA-Seq, Transcriptomics | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1 | -0 | -0 | -2 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -2 | -2 | -4015 | -425658 | -- |
- | ribowaltz | -ribowaltz_process, ribowaltz_plot | -Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data | -riboWaltz | -riboWaltz | -- | riboWaltz | -riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. | -- | Computational biology | -To update | -https://github.com/LabTranslationalArchitectomics/riboWaltz | -Transcriptomics, RNA | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz | -1.2.0 | -ribowaltz | -2.0 | -- | Computational biology | -0 | -0 | -2 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -14 | -161 | -- |
- | rsem | -extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie | -transcript quantification from RNA-Seq data | -- | - | - | - | - | - | - | To update | -https://github.com/deweylab/RSEM | -Transcriptomics, RNA | -rsem | -artbio | -https://github.com/artbio/tools-artbio/tree/master/tools/rsem | -https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem | -- | rsem | -1.3.3 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -67 | -377 | -- |
- | rseqc | -rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin | -an RNA-seq quality control package | -rseqc | -rseqc | -- | RSeQC | -Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. | -Data handling | -Sequencing | -Up-to-date | -https://code.google.com/p/rseqc/ | -Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization | -rseqc | -nilesh | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc | -5.0.3 | -rseqc | -5.0.3 | -Data handling | -Sequencing | -22 | -22 | -22 | -22 | -22 | -22 | -22 | -22 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -22 | -0 | -0 | -0 | -22 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -22 | -22 | -3206 | -133498 | -- |
- | ruvseq | -ruvseq | -Remove Unwanted Variation from RNA-Seq Data | -ruvseq | -ruvseq | -- | RUVSeq | -This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. | -Differential gene expression analysis | -Gene expression, RNA-seq | -To update | -https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html | -Transcriptomics, RNA, Statistics | -ruvseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq | -1.26.0 | -bioconductor-ruvseq | -1.36.0 | -Differential gene expression analysis | -Gene expression | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -76 | -1236 | -- |
- | salmon | -alevin, salmon, salmonquantmerge | -Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. | -salmon | -salmon | -- | Salmon | -A tool for transcript expression quantification from RNA-seq data | -Sequence composition calculation, RNA-Seq quantification, Gene expression analysis | -RNA-Seq, Gene expression, Transcriptomics | -To update | -https://github.com/COMBINE-lab/salmon | -Sequence Analysis, RNA, Transcriptomics | -- | bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/salmon | -https://github.com/bgruening/galaxytools/tree/master/tools/salmon | -1.10.1 | -salmon | -1.10.3 | -Sequence composition calculation, RNA-Seq quantification, Gene expression analysis | -RNA-Seq, Transcriptomics | -2 | -1 | -3 | -1 | -2 | -1 | -3 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -1 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -3 | -3 | -969 | -61937 | -- |
- | sashimi_plot | -sashimi_plot | -Generates a sashimi plot from bam files. | -- | - | - | - | - | - | - | To update | -http://artbio.fr | -RNA, Transcriptomics, Graphics, Visualization | -sashimi_plot | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot | -https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot | -0.1.1 | -python | -- | - | - | 0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -- |
- | sc3 | -sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare | -De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. | -- | - | - | - | - | - | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_sc3 | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 | -1.8.0 | -sc3-scripts | -0.0.6 | -- | - | 0 | -0 | -7 | -0 | -0 | -0 | -7 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -9 | -- |
- | scanpy | -scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders | -Scanpy – Single-Cell Analysis in Python | -scanpy | -scanpy | -- | SCANPY | -Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. | -Differential gene expression analysis | -Gene expression, Cell biology, Genetics | -To update | -https://scanpy.readthedocs.io | -Transcriptomics, Sequence Analysis | -scanpy | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy | -1.9.6 | -scanpy | -1.7.2 | -Differential gene expression analysis | -Gene expression, Cell biology, Genetics | -6 | -6 | -6 | -0 | -6 | -6 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -6 | -6 | -766 | -51978 | -- |
- | scanpy | -anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data | -scanpy-scripts, command-line wrapper scripts around Scanpy. | -- | - | - | - | - | - | - | To update | -https://scanpy.readthedocs.io | -Transcriptomics, Sequence Analysis, RNA | -scanpy_scripts | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy | -1.9.3 | -scanpy-scripts | -1.9.301 | -- | - | 22 | -27 | -27 | -0 | -22 | -27 | -27 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -14 | -13 | -2185 | -39356 | -- |
- | scater | -scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results | -De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. | -- | - | - | - | - | - | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_scater | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater | -1.10.0 | -scater-scripts | -0.0.5 | -- | - | 0 | -1 | -6 | -0 | -0 | -1 | -6 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -16 | -387 | -- |
- | scater | -scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne | -Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. | -scater | -scater | -- | scater | -Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. | -Read pre-processing, Sequencing quality control, Sequence visualisation | -RNA-seq, Quality affairs, Molecular genetics | -To update | -http://bioconductor.org/packages/scater/ | -Transcriptomics, RNA, Visualization | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater | -1.22.0 | -bioconductor-scater | -1.30.1 | -Read pre-processing, Sequence visualisation | -Quality affairs, Molecular genetics | -0 | -5 | -5 | -0 | -0 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -77 | -1365 | -- |
- | sccaf | -run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out | -SCCAF: Single Cell Clustering Assessment Framework. | -- | - | - | - | - | - | - | To update | -https://github.com/sccaf/sccaf | -Transcriptomics | -SCCAF | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf | -0.0.9 | -sccaf | -0.0.10 | -- | - | 0 | -0 | -4 | -0 | -0 | -0 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -110 | -- |
- | sceasy | -sceasy_convert | -Converter between difference single-cell formats | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/cellgeni/sceasy/ | -Transcriptomics | -sceasy_convert | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy | -0.0.7 | -r-sceasy | -0.0.7 | -- | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -90 | -721 | -- |
- | sceasy | -sceasy_convert | -Convert scRNA data object between popular formats | -- | - | - | - | - | - | - | To update | -- | Transcriptomics | -sceasy | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy | -0.0.5 | -r-sceasy | -0.0.7 | -- | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -90 | -721 | -- |
- | schicexplorer | -schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol | -scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. | -- | - | - | - | - | - | - | To update | -https://github.com/joachimwolff/schicexplorer | -Sequence Analysis, Transcriptomics, Visualization | -schicexplorer | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer | -4 | -schicexplorer | -7 | -- | - | 0 | -0 | -16 | -0 | -0 | -0 | -16 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -16 | -16 | -23 | -779 | -- |
- | scmap | -scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features | -De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. | -- | - | - | - | - | - | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_scmap | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap | -1.6.4 | -scmap-cli | -0.1.0 | -- | - | 0 | -0 | -7 | -0 | -0 | -0 | -7 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -13 | -83 | -- |
- | scpipe | -scpipe | -A flexible preprocessing pipeline for single-cell RNA-sequencing data | -scpipe | -scpipe | -- | scPipe | -A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. | -Genome annotation, Validation, Alignment, Visualisation | -Gene expression, RNA-Seq, Sequencing | -To update | -http://bioconductor.org/packages/release/bioc/html/scPipe.html | -Transcriptomics, RNA, Statistics | -scpipe | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe | -1.0.0+galaxy2 | -bioconductor-scpipe | -2.2.0 | -Genome annotation, Validation, Alignment, Visualisation | -Gene expression, RNA-Seq | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -11 | -628 | -- |
- | scpred | -scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model | -De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 | -- | - | - | - | - | - | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_scpred | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred | -1.0.2 | -scpred-cli | -0.1.0 | -- | - | 0 | -0 | -4 | -0 | -0 | -0 | -4 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -4 | -25 | -- |
- | seurat | -seurat | -A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data | -- | - | - | - | - | - | - | To update | -https://github.com/satijalab/seurat | -Transcriptomics, RNA, Statistics | -seurat | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat | -4.3.0.1 | -r-seurat | -3.0.2 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -66 | -1543 | -- |
- | seurat | -seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features | -De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_seurat | -ebi-gxa | -- | https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat | -4.0.0 | -seurat-scripts | -4.0.0 | -- | - | 0 | -0 | -14 | -11 | -0 | -0 | -14 | -11 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -19 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -181 | -1966 | -- |
- | slamdunk | -alleyoop, slamdunk | -Slamdunk maps and quantifies SLAMseq reads | -- | - | - | - | - | - | - | Up-to-date | -http://t-neumann.github.io/slamdunk | -RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers | -slamdunk | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk | -0.4.3 | -slamdunk | -0.4.3 | -- | - | 2 | -0 | -2 | -0 | -2 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -2 | -2 | -361 | -- |
- | sleuth | -sleuth | -Sleuth is a program for differential analysis of RNA-Seq data. | -sleuth | -sleuth | -- | sleuth | -A statistical model and software application for RNA-seq differential expression analysis. | -Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation | -RNA-seq, Gene expression, Statistics and probability | -Up-to-date | -https://github.com/pachterlab/sleuth | -Transcriptomics, RNA, Statistics | -sleuth | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth | -0.30.1 | -r-sleuth | -0.30.1 | -Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation | -Gene expression, Statistics and probability | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -8 | -64 | -- |
- | star_fusion | -star_fusion | -STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR | -- | - | - | - | - | - | - | To update | -- | Sequence Analysis, Transcriptomics | -star_fusion | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion | -0.5.4-3+galaxy1 | -star-fusion | -1.13.0 | -- | - | 1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -35 | -1212 | -- |
- | stringtie | -stringtie, stringtie_merge | -StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. | -stringtie | -stringtie | -- | StringTie | -Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. | -Transcriptome assembly, RNA-Seq analysis | -Transcriptomics, RNA-seq | -Up-to-date | -http://ccb.jhu.edu/software/stringtie/ | -Transcriptomics | -stringtie | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie | -2.2.3 | -stringtie | -2.2.3 | -Transcriptome assembly, RNA-Seq analysis | -Transcriptomics | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -2 | -0 | -0 | -2 | -2 | -2165 | -167659 | -- |
- | tophat_fusion_post | -tophat_fusion_post | -Wrapper for Tophat-Fusion post step | -- | - | - | - | - | - | - | To update | -- | Transcriptomics | -tophat_fusion_post | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post | -0.1 | -blast+ | -- | - | - | 0 | -1 | -1 | -0 | -0 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -15 | -216 | -- |
- | transdecoder | -transdecoder | -TransDecoder finds coding regions within transcripts | -TransDecoder | -TransDecoder | -- | TransDecoder | -TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. | -Coding region prediction, de Novo sequencing, De-novo assembly | -Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing | -To update | -https://transdecoder.github.io/ | -Transcriptomics, RNA | -transdecoder | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder | -5.5.0 | -transdecoder | -5.7.1 | -Coding region prediction, de Novo sequencing, De-novo assembly | -Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -348 | -5468 | -- |
- | trinity | -trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats | -Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq | -trinity | -trinity | -- | Trinity | -Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. | -Transcriptome assembly | -Transcriptomics, Gene expression, Gene transcripts | -Up-to-date | -https://github.com/trinityrnaseq/trinityrnaseq | -Transcriptomics, RNA | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity | -2.15.1 | -trinity | -2.15.1 | -Transcriptome assembly | -Transcriptomics, Gene transcripts | -9 | -13 | -13 | -13 | -9 | -13 | -13 | -13 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -2 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -11 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -13 | -12 | -1762 | -31951 | -- |
- | trinotate | -trinotate | -Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. | -trinotate | -trinotate | -- | Trinotate | -Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. | -Gene functional annotation | -Gene expression, Transcriptomics | -To update | -https://trinotate.github.io/ | -Transcriptomics, RNA | -trinotate | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate | -3.2.2 | -trinotate | -4.0.2 | -Gene functional annotation | -Transcriptomics | -1 | -1 | -1 | -0 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -151 | -1796 | -- |
- | tximport | -tximport | -Wrapper for the Bioconductor package tximport | -tximport | -tximport | -- | tximport | -An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. | -Pathway or network analysis, Formatting, RNA-Seq analysis | -Transcriptomics, Gene transcripts, Workflows | -To update | -http://bioconductor.org/packages/tximport/ | -Transcriptomics | -tximport | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport | -1.22.0 | -bioconductor-tximport | -1.30.0 | -Pathway or network analysis, Formatting, RNA-Seq analysis | -Transcriptomics, Gene transcripts, Workflows | -1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -88 | -1408 | -- |
- | ucsc-cell-browser | -ucsc_cell_browser | -Python pipeline and Javascript scatter plot library for single-cell datasets | -- | - | - | - | - | - | - | To update | -https://cells.ucsc.edu/ | -Transcriptomics | -ucsc_cell_browser | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser | -1.0.0+galaxy1 | -ucsc-cell-browser | -1.2.6 | -- | - | 0 | -0 | -1 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -78 | -941 | -- |
- | umi_tools | -umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist | -UMI-tools extract - Extract UMIs from fastq | -umi-tools | -umi-tools | -- | UMI-tools | -Tools for handling Unique Molecular Identifiers in NGS data sets. | -Sequencing quality control | -NGS, Sequence sites, features and motifs, Quality affairs | -To update | -https://github.com/CGATOxford/UMI-tools | -Sequence Analysis, Transcriptomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools | -1.1.2 | -umi_tools | -1.1.5 | -Sequencing quality control | -Sequence sites, features and motifs, Quality affairs | -5 | -5 | -5 | -5 | -5 | -5 | -5 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -5 | -5 | -379 | -61618 | -- |
- | velocyto | -velocyto_cli | -Velocyto is a library for the analysis of RNA velocity. | -- | - | - | - | - | - | - | Up-to-date | -http://velocyto.org/ | -Transcriptomics | -velocyto | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto | -0.17.17 | -velocyto.py | -0.17.17 | -- | - | 1 | -0 | -1 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -2 | -- |
- | volcanoplot | -volcanoplot | -Tool to create a Volcano Plot | -- | - | - | - | - | - | - | To update | -https://ggplot2.tidyverse.org/ | -Visualization, Transcriptomics, Statistics | -volcanoplot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot | -0.0.6 | -r-ggplot2 | -2.2.1 | -- | - | 1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -0 | -1 | -1 | -1749 | -30946 | -- |
Expand | -Galaxy wrapper id | -Galaxy wrapper version | -Conda version | -Conda id | -Status | -bio.tool id | -bio.tool name | -EDAM operation | -EDAM topic | -Description | -bio.tool description | -biii | -Status | -Source | -ToolShed categories | -ToolShed id | -Galaxy wrapper owner | -Galaxy wrapper source | -
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
- | askor | -0.2 | -3.58.1 | -bioconductor-limma | -To update | -- | - | - | - | AskoR links EdgeR and AskOmics | -- | - | To update | -https://github.com/askomics/askoR | -Transcriptomics | -askor_de | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/askor | -
- | baric_archive | -1.1.0 | -- | - | To update | -- | - | - | - | A data source tool to fetch data from a BARIC Archive server. | -- | - | To update | -https://www.cesgo.org/catibaric/ | -Data Source | -- | genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive | -
- | braker | -2.1.6 | -- | - | To update | -- | - | - | - | BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . | -- | - | To update | -https://github.com/Gaius-Augustus/BRAKER | -Genome annotation | -braker | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/braker | -
- | braker3 | -3.0.8 | -- | - | To update | -- | - | - | - | BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . | -- | - | To update | -https://github.com/Gaius-Augustus/BRAKER | -Genome annotation | -braker3 | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/braker | -
- | feelnc2asko | -0.1 | -1.7.8 | -perl-bioperl | -To update | -- | - | - | - | Convert FeelNC GTF to GFF3 | -- | - | To update | -https://github.com/tderrien/FEELnc | -Convert Formats | -feelnc2asko | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko | -
- | gcms2isocor | -0.1.0 | -- | openjdk | -To update | -- | - | - | - | Conversion from GCMS PostRun Analysis to Isocor | -- | - | To update | -- | Metabolomics | -gcms2isocor | -genouest | -- |
- | get_pairs | -0.3 | -- | python | -To update | -- | - | - | - | Separate paired and unpaired reads from two fastq files | -- | - | To update | -- | Fastq Manipulation | -get_pairs | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs | -
- | helixer | -0.3.2 | -- | - | To update | -- | - | - | - | Gene calling with Deep Neural Networks | -- | - | To update | -https://github.com/weberlab-hhu/Helixer | -Genome annotation | -helixer | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/helixer | -
- | logol | -1.7.8 | -1.7.8 | -logol | -Up-to-date | -- | - | - | - | Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence | -- | - | Up-to-date | -http://logol.genouest.org/web/app.php/logol | -Sequence Analysis | -- | genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/logol | -
- | meneco | -1.5.2 | -1.5.2 | -meneco | -Up-to-date | -- | - | - | - | Meneco computes minimal completions to your draft network with reactions from a repair network | -- | - | Up-to-date | -http://bioasp.github.io/meneco/ | -Systems Biology | -meneco | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/meneco | -
- | miranda2asko | -0.2 | -- | perl | -To update | -- | - | - | - | Converts miRanda output into AskOmics format | -- | - | To update | -- | Convert Formats | -miranda2asko | -genouest | -https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko | -
- | openlabcds2csv | -0.1.0 | -- | openjdk | -To update | -- | - | - | - | Creates a summary of several "Internal Standard Report" OpenLabCDS results. | -- | - | To update | -- | Metabolomics | -openlabcds2csv | -genouest | -- |
- | peptimapper | -2.0 | -- | - | To update | -- | - | - | - | Proteogenomics workflow for the expert annotation of eukaryotic genomes | -- | - | To update | -https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 | -Proteomics | -- | genouest | -- |
- | Ensembl-REST | -0.1.2 | -- | requests | -To update | -- | - | - | - | A suite of Galaxy tools designed to work with Ensembl REST API. | -- | - | To update | -https://rest.ensembl.org | -Data Source | -- | earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST | -
- | GAFA | -0.3.1 | -- | - | To update | -- | - | - | - | Gene Align and Family Aggregator | -- | - | To update | -http://aequatus.tgac.ac.uk | -Visualization | -gafa | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ | -
- | TreeBest | -1.9.2.post0 | -1.9.2.post1 | -treebest | -To update | -- | - | - | - | TreeBeST best | -- | - | To update | -http://treesoft.sourceforge.net/treebest.shtml | -Phylogenetics | -treebest_best | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest | -
- | apoc | -1.0+galaxy1 | -1b16 | -apoc | -To update | -- | - | - | - | Large-scale structural comparison of protein pockets | -- | - | To update | -http://cssb.biology.gatech.edu/APoc | -Computational chemistry | -apoc | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ | -
- | blast_parser | -0.1.2 | -- | - | To update | -- | - | - | - | Convert 12- or 24-column BLAST output into 3-column hcluster_sg input | -- | - | To update | -https://github.com/TGAC/earlham-galaxytools/ | -Phylogenetics | -blast_parser | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser | -
- | ete | -3.1.2 | -3.1.1 | -ete3 | -To update | -- | - | - | - | Analyse phylogenetic trees using the ETE Toolkit | -- | - | To update | -http://etetoolkit.org/ | -Phylogenetics | -ete | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete | -
- | export_to_cluster | -0.0.2 | -- | EXPORT_DIR_PREFIX | -To update | -- | - | - | - | Export datasets to cluster | -- | - | To update | -https://github.com/TGAC/earlham-galaxytools/ | -Data Export | -export_to_cluster | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ | -
- | gblocks | -0.91b | -0.91b | -gblocks | -Up-to-date | -- | - | - | - | Gblocks | -- | - | Up-to-date | -http://molevol.cmima.csic.es/castresana/Gblocks.html | -Sequence Analysis | -gblocks | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks | -
- | gstf_preparation | -0.4.3 | -- | python | -To update | -- | - | - | - | GeneSeqToFamily preparation converts data for the workflow | -- | - | To update | -https://github.com/TGAC/earlham-galaxytools/ | -Convert Formats | -gstf_preparation | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation | -
- | hcluster_sg | -0.5.1.1 | -0.5.1 | -hcluster_sg | -To update | -- | - | - | - | Hierarchically clustering on a sparse graph | -- | - | To update | -https://github.com/douglasgscofield/hcluster | -Phylogenetics | -hcluster_sg | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg | -
- | hcluster_sg_parser | -0.2.1 | -- | - | To update | -- | - | - | - | Converts hcluster_sg 3-column output into lists of ids | -- | - | To update | -https://github.com/TGAC/earlham-galaxytools/ | -Phylogenetics | -hcluster_sg_parser | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser | -
- | lotus2 | -2.32 | -2.32 | -lotus2 | -Up-to-date | -lotus2 | -lotus2 | -Sequence feature detection | -Metagenomics | -LotuS2 OTU processing pipeline | -LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. | -- | Up-to-date | -http://lotus2.earlham.ac.uk/ | -Metagenomics | -lotus2 | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 | -
- | miranda | -3.3a+galaxy1 | -3.3a | -miranda | -To update | -- | - | - | - | Finds potential target sites for miRNAs in genomic sequences | -- | - | To update | -http://www.microrna.org/ | -RNA | -miranda | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda | -
- | plotheatmap | -1.0 | -1.64.0 | -bioconductor-preprocesscore | -To update | -- | - | - | - | This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. | -- | - | To update | -- | Computational chemistry | -plotheatmap | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap | -
- | rdock | -1.0 | -2013.1 | -rDock | -To update | -- | - | - | - | Docking ligands to proteins and nucleic acids | -- | - | To update | -http://rdock.sourceforge.net/ | -Computational chemistry | -rdock | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ | -
- | replace_chromosome_names | -0.1 | -- | python | -To update | -- | - | - | - | Replace chromosome names | -- | - | To update | -- | Text Manipulation | -replace_chromosome_names | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ | -
- | rsat_filter_snps | -0.1 | -- | - | To update | -- | - | - | - | Filter SNPs in RSAT Matrix Scan output | -- | - | To update | -https://github.com/TGAC/earlham-galaxytools/ | -ChIP-seq, Systems Biology | -rsat_filter_snps | -earlham | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps | -
- | smart_domains | -0.1.0 | -1.7.8 | -perl-bioperl | -To update | -- | - | - | - | SMART domains | -- | - | To update | -http://smart.embl.de/ | -Sequence Analysis | -smart_domains | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains | -
- | smina | -1.0 | -2017.11.9 | -smina | -To update | -- | - | - | - | smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization | -- | - | To update | -https://sourceforge.net/projects/smina/ | -Computational chemistry | -smina | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ | -
- | t_coffee | -13.45.0.4846264 | -13.46.0.919e8c6b | -t-coffee | -To update | -- | - | - | - | T-Coffee | -- | - | To update | -http://www.tcoffee.org/ | -Sequence Analysis | -t_coffee | -earlhaminst | -https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee | -
- | abacas | -1.1 | -3.23 | -mummer | -To update | -- | - | - | - | Order and Orientate Contigs | -- | - | To update | -https://github.com/phac-nml/abacas | -Assembly | -abacas | -nml | -https://github.com/phac-nml/abacas | -
- | assemblystats | -1.1.0 | -1.7.8 | -perl-bioperl | -To update | -- | - | - | - | Summarise an assembly (e.g. N50 metrics) | -- | - | To update | -https://github.com/phac-nml/galaxy_tools | -Assembly | -assemblystats | -nml | -https://github.com/phac-nml/galaxy_tools | -
- | bam2mappingstats | -1.1.0 | -- | perl | -To update | -- | - | - | - | Generates mapping stats from a bam file. | -- | - | To update | -https://github.com/phac-nml/galaxy_tools | -Assembly | -bam2mappingstats | -nml | -https://github.com/phac-nml/galaxy_tools | -
- | bamclipper | -1.0.0 | -1.0.0 | -bamclipper | -Up-to-date | -- | - | - | - | Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. | -- | - | Up-to-date | -https://github.com/tommyau/bamclipper | -Sequence Analysis | -bamclipper | -nml | -https://github.com/tommyau/bamclipper | -
- | biohansel | -2.4.0 | -2.6.1 | -bio_hansel | -To update | -- | - | - | - | Heidelberg and Enteritidis SNP Elucidation | -- | - | To update | -https://github.com/phac-nml/biohansel | -Sequence Analysis | -biohansel | -nml | -https://github.com/phac-nml/biohansel | -
- | biohansel_bionumeric_converter | -0.2.0 | -- | pandas | -To update | -- | - | - | - | Convert BioHansel output data to a Bionumerics friendly form | -- | - | To update | -https://github.com/phac-nml/galaxy_tools | -Text Manipulation | -biohansel_bionumeric_converter | -nml | -- |
- | bundle_collections | -1.3.0 | -2.54 | -perl-getopt-long | -To update | -- | - | - | - | Tool to bundle up list collection into a single zip to be download | -- | - | To update | -- | Sequence Analysis | -bundle_collections | -nml | -- |
- | collapse_collection | -5.1.0 | -- | gawk | -To update | -- | - | - | - | Collection tool that collapses a list of files into a single datasset in order of appears in collection | -- | - | To update | -- | Sequence Analysis | -collapse_collections | -nml | -- |
- | combineJSON | -0.1 | -- | - | To update | -- | - | - | - | JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. | -- | - | To update | -- | Sequence Analysis | -combine_json | -nml | -- |
- | combine_assembly_stats | -1.0 | -2.54 | -perl-getopt-long | -To update | -- | - | - | - | Combine multiple Assemblystats datasets into a single tabular report | -- | - | To update | -https://github.com/phac-nml/galaxy_tools | -Assembly | -combine_assemblystats | -nml | -https://github.com/phac-nml/galaxy_tools | -
- | combine_tabular_collection | -0.1 | -- | - | To update | -- | - | - | - | Combine Tabular Collection into a single file | -- | - | To update | -- | Sequence Analysis | -combine_tabular_collection | -nml | -- |
- | concat_paired | -0.2 | -- | - | To update | -- | - | - | - | Concatenate paired datasets | -- | - | To update | -https://github.com/phac-nml/concat | -Text Manipulation | -concat_paired | -nml | -https://github.com/phac-nml/concat | -
- | cryptogenotyper | -1.0 | -1.0 | -cryptogenotyper | -Up-to-date | -- | - | - | - | CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. | -- | - | Up-to-date | -https://github.com/phac-nml/CryptoGenotyper | -Sequence Analysis | -cryptogenotyper | -nml | -https://github.com/phac-nml/CryptoGenotyper | -
- | csvtk | -0.20.0 | -0.29.0 | -csvtk | -To update | -- | - | - | - | Rapid data investigation and manipulation of csv/tsv files | -- | - | To update | -https://bioinf.shenwei.me/csvtk/ | -Text Manipulation | -csvtk | -nml | -https://github.com/shenwei356/csvtk | -
- | ectyper | -1.0.0 | -1.0.0 | -ectyper | -Up-to-date | -- | - | - | - | EC-Typer - in silico serotyping of Escherichia coli species | -- | - | Up-to-date | -https://github.com/phac-nml/ecoli_serotyping | -Sequence Analysis | -ectyper | -nml | -https://github.com/phac-nml/ecoli_serotyping | -
- | fasta2bed | -1.0.0 | -1.7.8 | -perl-bioperl | -To update | -- | - | - | - | Convert multiple fasta file into tabular bed file format | -- | - | To update | -https://github.com/phac-nml/galaxy_tools | -Sequence Analysis | -fasta2bed | -nml | -https://github.com/phac-nml/galaxy_tools | -
- | fasta_extract | -1.1.0 | -1.7.8 | -perl-bioperl | -To update | -- | - | - | - | extract single fasta from multiple fasta file | -- | - | To update | -https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract | -Sequence Analysis | -fasta_extract | -nml | -https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract | -
- | fastqc_stats | -1.2 | -1.7.8 | -perl-bioperl | -To update | -- | - | - | - | Summary multiple FastQC into a single tabular line report | -- | - | To update | -https://github.com/phac-nml/galaxy_tools | -Sequence Analysis | -fastqc_stats | -nml | -https://github.com/phac-nml/galaxy_tools | -
- | feht | -0.1.0 | -1.1.0 | -feht | -To update | -- | - | - | - | Automatically identify makers predictive of groups. | -- | - | To update | -https://github.com/phac-nml/galaxy_tools | -Sequence Analysis | -feht | -nml | -https://github.com/phac-nml/galaxy_tools | -
- | filter_spades_repeats | -1.0.1 | -1.7.8 | -perl-bioperl | -To update | -- | - | - | - | Remove short and repeat contigs/scaffolds | -- | - | To update | -https://github.com/phac-nml/galaxy_tools/ | -Assembly | -filter_spades_repeats | -nml | -https://github.com/phac-nml/galaxy_tools/ | -
- | getmlst | -0.1.4.1 | -0.2.0 | -srst2 | -To update | -- | - | - | - | Download MLST datasets by species from pubmlst.org | -- | - | To update | -- | Sequence Analysis | -getmlst | -nml | -- |
- | gnali | -1.1.0 | -1.1.0 | -gnali | -Up-to-date | -- | - | - | - | A tool to find nonessential, loss-of-function gene variants | -- | - | Up-to-date | -https://github.com/phac-nml/gnali/ | -Variant Analysis | -gnali | -nml | -https://github.com/phac-nml/gnali/ | -
- | hivtrace | -1.0.1 | -1.5.0 | -hivtrace | -To update | -- | - | - | - | An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. | -- | - | To update | -- | Sequence Analysis | -hivtrace | -nml | -https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace | -
- | kaptive | -0.3.0 | -2.0.6 | -kaptive | -To update | -- | - | - | - | Kaptive reports information about capsular (K) loci found in genome assemblies. | -- | - | To update | -- | Sequence Analysis | -kaptive | -nml | -- |
- | kat_filter | -2.3 | -2.4.2 | -kat | -To update | -- | - | - | - | Filtering kmers or reads from a database of kmers hashes | -- | - | To update | -- | Sequence Analysis | -kat_filter | -nml | -- |
- | kat_sect | -2.3 | -2.4.2 | -kat | -To update | -- | - | - | - | SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. | -- | - | To update | -- | - | kat_sect | -nml | -- |
- | mauve_contig_mover | -1.0.10 | -2.4.0.r4736 | -mauve | -To update | -- | - | - | - | Order a draft genome relative to a related reference genome | -- | - | To update | -https://github.com/phac-nml/mauve_contig_mover | -Sequence Analysis | -mauve_contig_mover | -nml | -https://github.com/phac-nml/mauve_contig_mover | -
- | mob_suite | -3.0.3 | -3.1.8 | -mob_suite | -To update | -- | - | - | - | MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies | -- | - | To update | -https://github.com/phac-nml/mob-suite | -Sequence Analysis | -mob_suite | -nml | -https://github.com/phac-nml/mob-suite | -
- | mrbayes | -1.0.2 | -3.2.7 | -mrbayes | -To update | -- | - | - | - | A program for the Bayesian estimation of phylogeny. | -- | - | To update | -- | Sequence Analysis | -mrbayes | -nml | -- |
- | mykrobe_parser | -0.1.4.1 | -- | r-base | -To update | -- | - | - | - | RScript to parse the results of mykrobe predictor. | -- | - | To update | -https://github.com/phac-nml/mykrobe-parser | -Sequence Analysis | -mykrobe_parser | -nml | -https://github.com/phac-nml/mykrobe-parser | -
- | pangolin | -1.1.14 | -4.3 | -pangolin | -To update | -- | - | - | - | Phylogenetic Assignment of Named Global Outbreak LINeages | -- | - | To update | -https://github.com/hCoV-2019/pangolin | -Sequence Analysis | -pangolin | -nml | -https://github.com/hCoV-2019/pangolin | -
- | patrist | -0.1.2 | -- | python | -To update | -- | - | - | - | Extract Patristic Distance From a Tree | -- | - | To update | -https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 | -Phylogenetics | -patrist | -nml | -https://github.com/phac-nml/patrist | -
- | plasmid_profiler | -0.1.6 | -- | r | -To update | -- | - | - | - | Explores plasmid content in WGS data | -- | - | To update | -- | - | plasmid_profiler | -nml | -- |
- | plasmid_profiler_suite | -- | - | - | To update | -- | - | - | - | Plasmid Profiler suite defining all dependencies for Plasmid Profiler | -- | - | To update | -- | Sequence Analysis | -suite_plasmid_profiler | -nml | -- |
- | plasmidspades | -1.1 | -3.15.5 | -spades | -To update | -- | - | - | - | Genome assembler for assemblying plasmid | -- | - | To update | -- | Assembly | -plasmidspades | -nml | -- |
- | pneumocat | -1.2.1 | -1.2.1 | -pneumocat | -Up-to-date | -- | - | - | - | Pneumococcal Capsular Typing of illumina fastq reads | -- | - | Up-to-date | -https://github.com/phe-bioinformatics/PneumoCaT | -Variant Analysis | -pneumocat | -nml | -https://github.com/phe-bioinformatics/PneumoCaT | -
- | promer | -1.2 | -- | python | -To update | -- | - | - | - | Aligns two sets of contigs and reports amino acid substitutions between them | -- | - | To update | -https://github.com/phac-nml/promer | -Assembly | -promer | -nml | -https://github.com/phac-nml/promer | -
- | pseudogenome | -1.0.0 | -1.7.8 | -perl-bioperl | -To update | -- | - | - | - | Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. | -- | - | To update | -https://github.com/phac-nml/galaxy_tools | -Sequence Analysis | -pseudogenome | -nml | -- |
- | quasitools | -0.7.0 | -0.7.0 | -quasitools | -Up-to-date | -- | - | - | - | A collection of tools for analysing Viral Quasispecies | -- | - | Up-to-date | -https://github.com/phac-nml/quasitools | -Sequence Analysis | -quasitools | -nml | -https://github.com/phac-nml/quasitools | -
- | refseq_masher | -0.1.2 | -0.1.2 | -refseq_masher | -Up-to-date | -- | - | - | - | Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. | -- | - | Up-to-date | -https://github.com/phac-nml/refseq_masher | -Sequence Analysis | -refseq_masher | -nml | -https://github.com/phac-nml/refseq_masher | -
- | seqtk_nml | -1.0.1 | -1.4 | -seqtk | -To update | -- | - | - | - | Tool to downsample fastq reads | -- | - | To update | -https://github.com/lh3/seqtk | -Sequence Analysis | -seqtk_nml | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | sistr_cmd | -1.1.1 | -1.1.1 | -sistr_cmd | -Up-to-date | -- | - | - | - | SISTR in silico serotyping tool | -- | - | Up-to-date | -https://github.com/phac-nml/sistr_cmd | -Sequence Analysis | -sistr_cmd | -nml | -- |
- | smalt | -0.7.6 | -0.7.6 | -smalt | -Up-to-date | -- | - | - | - | SMALT aligns DNA sequencing reads with a reference genome. | -- | - | Up-to-date | -http://www.sanger.ac.uk/science/tools/smalt-0 | -Sequence Analysis | -smalt | -nml | -https://sourceforge.net/projects/smalt/ | -
- | spades_header_fixer | -1.1.2+galaxy1 | -- | sed | -To update | -- | - | - | - | Fixes Spades Fasta ids | -- | - | To update | -https://github.com/phac-nml/galaxy_tools | -Fasta Manipulation | -spades_fasta_header_fixer | -nml | -https://github.com/phac-nml/galaxy_tools | -
- | spatyper | -0.3.3 | -0.3.3 | -spatyper | -Up-to-date | -- | - | - | - | Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. | -- | - | Up-to-date | -https://github.com/HCGB-IGTP/spaTyper | -Sequence Analysis | -spatyper | -nml | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper | -
- | spolpred | -1.0.1 | -- | spolpred | -To update | -- | - | - | - | A program for predicting the spoligotype from raw sequence reads | -- | - | To update | -- | Sequence Analysis | -spolpred | -nml | -- |
- | srst2 | -0.3.7 | -0.2.0 | -srst2 | -To update | -- | - | - | - | Short Read Sequence Typing for Bacterial Pathogens | -- | - | To update | -- | Sequence Analysis | -srst2 | -nml | -- |
- | staramr | -0.10.0 | -0.10.0 | -staramr | -Up-to-date | -- | - | - | - | Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. | -- | - | Up-to-date | -https://github.com/phac-nml/staramr | -Sequence Analysis | -staramr | -nml | -https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr | -
- | stringmlst | -1.1.0 | -0.6.3 | -stringMLST | -To update | -- | - | - | - | Rapid and accurate identification of the sequence type (ST) | -- | - | To update | -- | Sequence Analysis | -stringmlst | -nml | -- |
- | tree_relabeler | -1.1.0 | -1.7.8 | -perl-bioperl | -To update | -- | - | - | - | Relabels the tips of a newick formatted tree. | -- | - | To update | -- | Text Manipulation | -tree_relabeler | -nml | -https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler | -
- | wade | -0.2.5+galaxy1 | -0.2.6 | -wade | -To update | -- | - | - | - | identify regions of interest | -- | - | To update | -https://github.com/phac-nml/wade | -Sequence Analysis | -wade | -nml | -https://github.com/phac-nml/wade | -
- | camera | -1.48.0 | -0.4_1 | -r-snow | -To update | -- | - | - | - | - | - | - | To update | -- | Metabolomics | -camera | -workflow4metabolomics | -- |
- | correlation_analysis | -1.0.1+galaxy0 | -1.1_4 | -r-batch | -To update | -- | - | - | - | [Metabolomics][W4M] Metabolites Correlation Analysis | -- | - | To update | -http://workflow4metabolomics.org | -Metabolomics | -correlation_analysis | -workflow4metabolomics | -https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ | -
- | genform | -- | r8 | -genform | -To update | -- | - | - | - | genform: generation of molecular formulas by high-resolution MS and MS/MS data | -- | - | To update | -https://sourceforge.net/projects/genform/ | -Metabolomics | -genform | -workflow4metabolomics | -https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ | -
- | influx_data_manager | -1.0.0 | -1.0.0 | -influx-si-data-manager | -Up-to-date | -- | - | - | - | Handling influx_si data inputs in Galaxy workflows | -- | - | Up-to-date | -https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ | -Metabolomics | -influx_si_data_manager | -workflow4metabolomics | -https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager | -
- | influx_si | -7.0.1 | -7.0.2 | -influx_si | -To update | -- | - | - | - | metabolic flux estimation based on [in]stationary labeling | -- | - | To update | -https://github.com/sgsokol/influx | -Metabolomics | -influx_si | -workflow4metabolomics | -https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ | -
- | ipo | -1.10.0 | -1.28.0 | -bioconductor-ipo | -To update | -- | - | - | - | [W4M][LC-MS] IPO | -- | - | To update | -https://github.com/rietho/IPO | -Metabolomics | -ipo | -lecorguille | -https://github.com/rietho/IPO | -
- | isoplot | -1.3.0+galaxy1 | -1.3.1 | -isoplot | -To update | -- | - | - | - | Isoplot is a software for the visualisation of MS data from C13 labelling experiments | -- | - | To update | -- | Metabolomics, Visualization | -isoplot | -workflow4metabolomics | -https://github.com/llegregam/Isoplot/tree/main | -
- | kmd_hmdb_data_plot | -1.0.0 | -- | python | -To update | -- | - | - | - | retrieves data from KMD HMDB API and produce plot and csv file | -- | - | To update | -https://github.com/workflow4metabolomics/tools-metabolomics | -Metabolomics | -kmd_hmdb_data_plot | -workflow4metabolomics | -https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ | -
- | mixmodel4repeated_measures | -3.1.0 | -- | r-lme4 | -To update | -- | - | - | - | [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model | -- | - | To update | -http://workflow4metabolomics.org | -Metabolomics | -mixmodel4repeated_measures | -workflow4metabolomics | -https://github.com/workflow4metabolomics/tools-metabolomics | -
- | ms2snoop | -2.2.1 | -- | r-base | -To update | -- | - | - | - | [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. | -- | - | To update | -http://workflow4metabolomics.org | -Metabolomics | -ms2snoop | -workflow4metabolomics | -- |
- | nmr_annotation | -3.0.0 | -1.1_4 | -r-batch | -To update | -- | - | - | - | [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation | -- | - | To update | -http://workflow4metabolomics.org | -Metabolomics | -nmr_annotation | -marie-tremblay-metatoul | -https://github.com/workflow4metabolomics/nmr_annotation | -
- | nmr_annotation2d | -2.0.0 | -1.1_4 | -r-batch | -To update | -- | - | - | - | [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra | -- | - | To update | -http://workflow4metabolomics.org | -Metabolomics | -2dnmrannotation | -marie-tremblay-metatoul | -https://github.com/workflow4metabolomics/tools-metabolomics | -
- | nmr_preprocessing | -- | 1.1_4 | -r-batch | -To update | -- | - | - | - | [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction | -- | - | To update | -http://workflow4metabolomics.org | -Metabolomics | -nmr_preprocessing | -marie-tremblay-metatoul | -https://github.com/workflow4metabolomics/nmr_preprocessing | -
- | normalization | -1.0.7 | -1.1_4 | -r-batch | -To update | -- | - | - | - | [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data | -- | - | To update | -http://workflow4metabolomics.org | -Metabolomics | -normalization | -marie-tremblay-metatoul | -https://github.com/workflow4metabolomics/normalization | -
- | physiofit | -3.3.2 | -3.3.2 | -physiofit | -Up-to-date | -- | - | - | - | PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes | -- | - | Up-to-date | -physiofit.readthedocs.io | -Metabolomics | -physiofit | -workflow4metabolomics | -https://github.com/MetaSys-LISBP/PhysioFit | -
- | physiofit_manager | -1.0.1 | -1.0.1 | -physiofit_data_manager | -Up-to-date | -- | - | - | - | Handling of physiofit input files | -- | - | Up-to-date | -https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager | -Metabolomics | -physiofit_manager | -workflow4metabolomics | -- |
- | xcms | -3.12.0 | -4.0.0 | -bioconductor-xcms | -To update | -- | - | - | - | - | - | - | To update | -https://github.com/sneumann/xcms | -Metabolomics | -xcms | -workflow4metabolomics | -https://github.com/workflow4metabolomics/tools-metabolomics/ | -
- | apollo | -- | 4.2.13 | -apollo | -To update | -- | - | - | - | Access an Apollo instance from Galaxy | -- | - | To update | -https://github.com/galaxy-genome-annotation/python-apollo | -Web Services | -- | gga | -https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo | -
- | askomics | -- | 0.5 | -askocli | -To update | -- | - | - | - | Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ | -- | - | To update | -https://github.com/askomics/ | -Web Services | -- | gga | -https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics | -
- | chado | -- | 2.3.9 | -python-chado | -To update | -- | - | - | - | Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado | -- | - | To update | -https://github.com/galaxy-genome-annotation/python-chado | -Web Services | -- | gga | -https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado | -
- | genenotebook | -0.4.13 | -0.4.13 | -genoboo | -Up-to-date | -- | - | - | - | Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io | -- | - | Up-to-date | -https://genenotebook.github.io | -Web Services | -- | gga | -https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook | -
- | jbrowse | -- | - | python | -To update | -- | - | - | - | A tool allowing to export a JBrowse dataset into a JBrowse docker container | -- | - | To update | -https://jbrowse.org | -Web Services | -jbrowse_to_container | -gga | -https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse | -
- | repeatexplorer2 | -2.3.8 | -- | - | To update | -- | - | - | - | Tool for annotation of repeats from unassembled shotgun reads. | -- | - | To update | -https://github.com/repeatexplorer/repex_tarean | -Genome annotation | -repeatexplorer2 | -gga | -https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 | -
- | tripal | -- | 3.2.1 | -python-tripal | -To update | -- | - | - | - | Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal | -- | - | To update | -https://github.com/galaxy-genome-annotation/python-tripal | -Web Services | -- | gga | -https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal | -
- | w4mcorcov | -0.98.18 | -- | r-base | -To update | -- | - | - | - | OPLS-DA Contrasts of Univariate Results | -- | - | To update | -https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper | -Metabolomics | -w4mcorcov | -eschen42 | -https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master | -
- | w4mclassfilter | -0.98.19 | -- | r-base | -To update | -- | - | - | - | Filter W4M data by values or metadata | -- | - | To update | -https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper | -Metabolomics | -w4mclassfilter | -eschen42 | -https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master | -
- | w4mjoinpn | -0.98.2 | -8.25 | -coreutils | -To update | -- | - | - | - | Join positive- and negative-mode W4M datasets | -- | - | To update | -https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper | -Metabolomics | -w4mjoinpn | -eschen42 | -https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master | -
- | 2d_auto_threshold | -0.0.5-2 | -- | scikit-image | -To update | -scikit-image | -scikit-image | -Image analysis, Image annotation, Visualisation, Data handling | -Imaging, Software engineering, Literature and language | -Automatic thresholding | -Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. | -scikit-image | -To update | -https://github.com/bmcv | -Imaging | -2d_auto_threshold | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ | -
- | 2d_feature_extraction | -0.1.1-2 | -- | pandas | -To update | -scikit-image | -scikit-image | -Image analysis, Image annotation, Visualisation, Data handling | -Imaging, Software engineering, Literature and language | -2D feature extraction | -Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. | -scikit-image | -To update | -https://github.com/bmcv | -Imaging | -2d_feature_extraction | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ | -
- | 2d_filter_segmentation_by_features | -0.0.1-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -filter segmentation by rules | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -2d_filter_segmentation_by_features | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ | -
- | 2d_histogram_equalization | -0.0.1-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -2d histogram equalization | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -2d_histogram_equalization | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ | -
- | 2d_simple_filter | -0.0.3-3 | -- | scikit-image | -To update | -scikit-image | -scikit-image | -Image analysis, Image annotation, Visualisation, Data handling | -Imaging, Software engineering, Literature and language | -2d simple filter | -Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. | -scikit-image | -To update | -https://github.com/bmcv | -Imaging | -2d_simple_filter | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ | -
- | 3d_tensor_feature_dimension_reduction | -0.0.1 | -- | numpy | -To update | -- | - | - | - | Dimensionality reduction for features (channels) of 3D tensor data using UMAP | -- | - | To update | -https://github.com/BMCV/galaxy-image-analysis | -Imaging | -3d_tensor_feature_dimension_reduction | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/ | -
- | anisotropic_diffusion | -0.2-2 | -- | scikit-image | -To update | -- | - | - | - | Anisotropic image diffusion | -- | - | To update | -https://github.com/bmcv | -Imaging | -anisotropic_diffusion | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ | -
- | bfconvert | -6.7.0+galaxy2 | -6.7.0 | -bftools | -To update | -- | - | - | - | Convert image | -- | python-bioformats | -To update | -https://github.com/bmcv | -Imaging, Convert Formats | -bfconvert | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ | -
- | binary2labelimage | -0.5 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Binary 2 label image | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -binary2labelimage | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ | -
- | binaryimage2points | -0.1-2 | -- | numpy | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Binary Image to Points | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -binaryimage2points | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ | -
- | bioformats2raw | -0.7.0 | -- | - | To update | -- | - | - | - | Convert image to OME-Zarr | -- | - | To update | -https://github.com/Euro-BioImaging | -Imaging, Convert Formats | -bioformats2raw | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw | -
- | color-deconvolution | -0.8-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Color-deconvolution methods | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -color_deconvolution | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/ | -
- | concat_channels | -0.2-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Concatenate images | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -concat_channels | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ | -
- | coordinates_of_roi | -0.0.4-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Coordinates of ROI | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -coordinates_of_roi | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ | -
- | count_objects | -0.0.5-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Count Objects | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -count_objects | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ | -
- | curl_post | -0.0.2 | -- | curl | -To update | -- | - | - | - | Send file via cURL POST | -- | - | To update | -https://github.com/bmcv | -Data Export, Web Services | -curl_post | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post | -
- | curve_fitting | -0.0.3-2 | -- | numpy | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Polynomial curve fitting to data points | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/BMCV/galaxy-image-analysis | -Imaging | -curve_fitting | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ | -
- | detection_viz | -0.3-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Detection Visualization | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -detection_viz | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ | -
- | image_info | -5.7.1 | -6.7.0 | -bftools | -To update | -- | - | - | - | Extracts image metadata | -- | python-bioformats | -To update | -https://github.com/bmcv | -Imaging | -image_info | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ | -
- | image_registration_affine | -0.0.3-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Intensity-based Image Registration | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -image_registration_affine | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ | -
- | imagecoordinates_flipaxis | -0.1-2 | -- | pandas | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Flip coordinate axes | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -imagecoordinates_flipaxis | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ | -
- | labelimage2points | -0.2-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Label Image to Points | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -labelimage2points | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ | -
- | landmark_registration | -0.1.0-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Landmark Registration | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -landmark_registration | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ | -
- | mahotas-features | -0.7-2 | -- | mahotas | -To update | -- | - | - | - | Compute image features using mahotas. | -- | mahotas-feature-computation | -To update | -https://github.com/luispedro/mahotas | -Imaging | -mahotas_features | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ | -
- | mergeneighboursinlabelimage | -0.3-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Merge Neighbours in Label Image | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -mergeneighboursinlabelimage | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage | -
- | overlay_images | -0.0.4 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Overlay two images | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/BMCV/galaxy-image-analysis | -Imaging | -overlay_images | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ | -
- | permutate_axis | -0.2-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Permutates axes | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -permutate_axis | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ | -
- | points2binaryimage | -0.2-1 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Points to Binary Image | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -points2binaryimage | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ | -
- | points2labelimage | -0.3-2 | -- | numpy | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Points to label image | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -points2labelimage | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ | -
- | points_association_nn | -0.0.3-2 | -- | numpy | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Association of points in consecutive frames | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/BMCV/galaxy-image-analysis | -Imaging | -points_association_nn | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ | -
- | projective_transformation | -0.1.2-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Projective transformation | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -projective_transformation | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ | -
- | projective_transformation_points | -0.1.1-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Projective transformation of ROIs defined by pixel (point) coordinates | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -projective_transformation_points | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ | -
- | rfove | -2023.11.12 | -- | - | To update | -rfove | -RFOVE | -Image analysis | -Cell biology, Biomedical science, Imaging | -Perform segmentation region-based fitting of overlapping ellipses | -RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. | -- | To update | -https://sites.google.com/site/costaspanagiotakis/research/cs | -Imaging | -rfove | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ | -
- | scale_image | -0.4-2 | -- | pillow | -To update | -scikit-image | -scikit-image | -Image analysis, Image annotation, Visualisation, Data handling | -Imaging, Software engineering, Literature and language | -Scale image | -Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. | -scikit-image | -To update | -https://github.com/bmcv | -Imaging | -scale_image | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ | -
- | segmetrics | -1.4 | -1.4.1 | -segmetrics | -To update | -segmetrics | -SegMetrics | -Image analysis | -- | Image segmentation and object detection performance measures | -Image segmentation and object detection performance measures | -segmetrics | -To update | -https://github.com/bmcv | -Imaging | -segmetrics | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ | -
- | slice_image | -0.3-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Slice image | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -slice_image | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ | -
- | split_labelmap | -0.2-2 | -- | scikit-image | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Split Labelmaps | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/bmcv | -Imaging | -split_labelmap | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ | -
- | spot_detection_2d | -0.0.3-2 | -- | imageio | -To update | -galaxy_image_analysis | -Galaxy Image Analysis | -Image analysis | -Imaging, Bioinformatics | -Spot detection in 2D image sequence | -Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. | -- | To update | -https://github.com/BMCV/galaxy-image-analysis | -Imaging | -spot_detection_2d | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ | -
- | superdsm | -0.2.0 | -0.2.0 | -superdsm | -Up-to-date | -superdsm | -SuperDSM | -Image analysis | -- | Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images | -SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. | -superdsm | -Up-to-date | -https://github.com/bmcv | -Imaging | -superdsm | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ | -
- | unzip | -6.0 | -- | unzip | -To update | -- | - | - | - | Unzip file | -- | - | To update | -https://github.com/bmcv | -Convert Formats | -unzip | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ | -
- | visceral-evaluatesegmentation | -0.5-2 | -2015.07.03 | -visceral-evaluatesegmentation | -To update | -- | - | - | - | Visceral Project - Evaluate Segmentation Tool | -- | evaluatesegmentation-tool | -To update | -https://github.com/bmcv | -Imaging | -visceral_evaluatesegmentation | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation | -
- | wsi_extract_top_view | -0.2-2 | -- | scikit-image | -To update | -- | - | - | - | WSI Extract Top View | -- | - | To update | -https://github.com/bmcv | -Imaging | -wsi_extract_top_view | -imgteam | -https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ | -
- | add_value | -1.0.1 | -- | perl | -To update | -- | - | - | - | Add a value as a new column. | -- | - | To update | -- | Text Manipulation | -add_value | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value | -
- | annotation_profiler | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Profile Annotations for a set of genomic intervals | -- | - | To update | -- | Genomic Interval Operations | -annotation_profiler | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler | -
- | best_regression_subsets | -1.0.0 | -- | numpy | -To update | -- | - | - | - | Perform Best-subsets Regression | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -best_regression_subsets | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets | -
- | blat_coverage_report | -1.0.0 | -- | - | To update | -- | - | - | - | Polymorphism of the Reads | -- | - | To update | -- | Next Gen Mappers, Sequence Analysis | -blat_coverage_report | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report | -
- | blat_mapping | -1.0.0 | -- | - | To update | -- | - | - | - | Coverage of the Reads in wiggle format | -- | - | To update | -- | Next Gen Mappers, Sequence Analysis | -blat_mapping | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping | -
- | bowtie_wrappers | -1.2.0 | -1.3.1 | -bowtie | -To update | -- | - | - | - | Galaxy wrappers for the Bowtie short read mapping tools. | -- | - | To update | -http://bowtie-bio.sourceforge.net/ | -Next Gen Mappers | -bowtie_wrappers | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers | -
- | canonical_correlation_analysis | -1.0.0 | -- | R | -To update | -- | - | - | - | Canonical Correlation Analysis | -- | - | To update | -- | Statistics | -canonical_correlation_analysis | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis | -
- | categorize_elements_satisfying_criteria | -1.0.0 | -- | - | To update | -- | - | - | - | Categorize Elements satisfying criteria. | -- | - | To update | -- | Statistics | -categorize_elements_satisfying_criteria | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria | -
- | ccat | -0.0.2 | -3.0 | -ccat | -To update | -- | - | - | - | Control-based ChIP-seq Analysis Tool | -- | - | To update | -- | ChIP-seq | -ccat | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat | -
- | cd_hit_dup | -0.0.1 | -4.8.1 | -cd-hit-auxtools | -To update | -- | - | - | - | simple tool for removing duplicates from sequencing reads | -- | - | To update | -- | Metagenomics, Sequence Analysis | -cd_hit_dup | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup | -
- | change_case | -1.0.1 | -- | perl | -To update | -- | - | - | - | Convert column case. | -- | - | To update | -- | Text Manipulation | -change_case | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case | -
- | compute_motif_frequencies_for_all_motifs | -1.0.0 | -- | - | To update | -- | - | - | - | Compute Motif Frequencies For All Motifs, motif by motif. | -- | - | To update | -- | Sequence Analysis, Statistics | -compute_motif_frequencies_for_all_motifs | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs | -
- | compute_motifs_frequency | -1.0.0 | -- | - | To update | -- | - | - | - | Compute Motif Frequencies in indel flanking regions. | -- | - | To update | -- | Sequence Analysis, Statistics | -compute_motifs_frequency | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency | -
- | compute_q_values | -1.0.1 | -- | R | -To update | -- | - | - | - | Compute q-values based on multiple simultaneous tests p-values | -- | - | To update | -- | Statistics | -compute_q_values | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values | -
- | condense_characters | -1.0.0 | -- | - | To update | -- | - | - | - | Condense consecutive characters. | -- | - | To update | -- | Text Manipulation | -condense_characters | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters | -
- | convert_characters | -1.0.1 | -- | python | -To update | -- | - | - | - | Convert delimiters to tab. | -- | - | To update | -- | Text Manipulation | -convert_characters | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters | -
- | convert_solid_color2nuc | -1.0.0 | -- | - | To update | -- | - | - | - | Convert Color Space to Nucleotides | -- | - | To update | -- | Fasta Manipulation | -convert_solid_color2nuc | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc | -
- | correlation | -1.0.0 | -- | rpy | -To update | -- | - | - | - | Correlation for numeric columns | -- | - | To update | -- | Statistics | -correlation | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation | -
- | count_gff_features | -0.2 | -1.1.0 | -galaxy-ops | -To update | -- | - | - | - | Count GFF Features | -- | - | To update | -- | Sequence Analysis | -count_gff_features | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features | -
- | ctd_batch | -1.0.0 | -- | - | To update | -- | - | - | - | CTD analysis of chemicals, diseases, or genes | -- | - | To update | -- | Sequence Analysis | -ctd_batch | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch | -
- | cummerbund | -2.16.0 | -- | fonts-conda-ecosystem | -To update | -- | - | - | - | Wrapper for the Bioconductor cummeRbund library | -- | - | To update | -https://bioconductor.org/packages/release/bioc/html/cummeRbund.html | -RNA, Visualization | -cummerbund | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund | -
- | cummerbund_to_tabular | -1.0.1 | -- | - | To update | -- | - | - | - | Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. | -- | - | To update | -- | Convert Formats, Next Gen Mappers | -cummerbund_to_tabular | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular | -
- | cut_columns | -1.0.2 | -- | - | To update | -- | - | - | - | Select columns from a dataset. | -- | - | To update | -- | Text Manipulation | -cut_columns | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns | -
- | delete_overlapping_indels | -1.0.0 | -- | - | To update | -- | - | - | - | Delete Overlapping Indels from a chromosome indels file | -- | - | To update | -- | Sequence Analysis | -delete_overlapping_indels | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels | -
- | dgidb_annotator | -0.1 | -- | - | To update | -- | - | - | - | Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) | -- | - | To update | -- | Systems Biology, Variant Analysis | -dgidb_annotator | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator | -
- | divide_pg_snp | -1.0.0 | -- | - | To update | -- | - | - | - | Separate pgSnp alleles into columns | -- | - | To update | -- | Sequence Analysis | -divide_pg_snp | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp | -
- | draw_stacked_barplots | -1.0.0 | -- | R | -To update | -- | - | - | - | Draw Stacked Bar Plots for different categories and different criteria | -- | - | To update | -- | Graphics, Statistics | -draw_stacked_barplots | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots | -
- | dwt_cor_ava_perclass | -1.0.1 | -1.7.5 | -r-waveslim | -To update | -- | - | - | - | Compute P-values and Correlation Coefficients for Feature Occurrences | -- | - | To update | -- | Statistics | -dwt_cor_ava_perclass | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass | -
- | dwt_cor_avb_all | -1.0.1 | -1.7.5 | -r-waveslim | -To update | -- | - | - | - | Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features | -- | - | To update | -- | Statistics | -dwt_cor_avb_all | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all | -
- | dwt_ivc_all | -1.0.1 | -1.7.5 | -r-waveslim | -To update | -- | - | - | - | Compute P-values and Second Moments for Feature Occurrences | -- | - | To update | -- | Statistics | -dwt_ivc_all | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all | -
- | dwt_var_perclass | -1.0.1 | -1.7.5 | -r-waveslim | -To update | -- | - | - | - | Compute P-values and Max Variances for Feature Occurrences | -- | - | To update | -- | Statistics | -dwt_var_perclass | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass | -
- | dwt_var_perfeature | -1.0.2 | -- | r-bitops | -To update | -- | - | - | - | Wavelet variance using Discrete Wavelet Transfoms | -- | - | To update | -- | Statistics | -dwt_var_perfeature | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature | -
- | express | -1.1.1 | -1.5.1 | -eXpress | -To update | -- | - | - | - | Quantify the abundances of a set of target sequences from sampled subsequences | -- | - | To update | -- | RNA | -express | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/express | -
- | fasta_compute_length | -1.0.3 | -- | python | -To update | -- | - | - | - | Compute sequence length | -- | - | To update | -- | Fasta Manipulation | -fasta_compute_length | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length | -
- | fasta_concatenate_by_species | -0.0.1 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Concatenate FASTA alignment by species | -- | - | To update | -- | Fasta Manipulation | -fasta_concatenate_by_species | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species | -
- | fasta_filter_by_length | -1.2 | -- | python | -To update | -- | - | - | - | Filter sequences by length | -- | - | To update | -- | Fasta Manipulation | -fasta_filter_by_length | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length | -
- | fasta_to_tabular | -1.1.1 | -- | python | -To update | -- | - | - | - | FASTA-to-Tabular converter | -- | - | To update | -- | Fasta Manipulation | -fasta_to_tabular | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular | -
- | fastq_trimmer_by_quality | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | FASTQ Quality Trimmer by sliding window | -- | - | Up-to-date | -- | Fastq Manipulation | -fastq_trimmer_by_quality | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality | -
- | fastqsolexa_to_fasta_qual | -1.0.0 | -- | - | To update | -- | - | - | - | FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data | -- | - | To update | -- | Convert Formats, Fastq Manipulation | -fastqsolexa_to_fasta_qual | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual | -
- | featurecounter | -2.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Feature coverage | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -featurecounter | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter | -
- | filter_transcripts_via_tracking | -0.1 | -- | - | To update | -- | - | - | - | Filter Combined Transcripts | -- | - | To update | -- | RNA | -filter_transcripts_via_tracking | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking | -
- | generate_pc_lda_matrix | -1.0.0 | -- | - | To update | -- | - | - | - | Generate a Matrix for using PC and LDA | -- | - | To update | -- | Sequence Analysis | -generate_pc_lda_matrix | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix | -
- | getindelrates_3way | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Estimate Indel Rates for 3-way alignments | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -getindelrates_3way | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way | -
- | getindels_2way | -1.0.0 | -- | numpy | -To update | -- | - | - | - | Fetch Indels from pairwise alignments | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -getindels_2way | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way | -
- | gmaj | -2.0.1 | -- | - | To update | -- | - | - | - | GMAJ Multiple Alignment Viewer | -- | - | To update | -- | Visualization | -gmaj | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj | -
- | hisat | -1.0.3 | -- | hisat | -To update | -- | - | - | - | HISAT is a fast and sensitive spliced alignment program. | -- | - | To update | -http://ccb.jhu.edu/software/hisat/index.shtml | -Assembly | -hisat | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat | -
- | histogram | -1.0.4 | -2.7.8 | -rpy2 | -To update | -- | - | - | - | Histogram of a numeric column | -- | - | To update | -- | Graphics, Statistics | -histogram | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram | -
- | indels_3way | -1.0.3 | -- | - | To update | -- | - | - | - | Fetch Indels from 3-way alignments | -- | - | To update | -- | Sequence Analysis | -indels_3way | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way | -
- | kernel_canonical_correlation_analysis | -1.0.0 | -- | rpy | -To update | -- | - | - | - | Kernel Canonical Correlation Analysis | -- | - | To update | -- | Statistics | -kernel_canonical_correlation_analysis | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis | -
- | kernel_principal_component_analysis | -1.0.0 | -- | rpy | -To update | -- | - | - | - | Kernel Principal Component Analysis | -- | - | To update | -- | Statistics | -kernel_principal_component_analysis | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis | -
- | lastz_paired_reads | -1.1.1 | -1.04.22 | -lastz | -To update | -- | - | - | - | Galaxy wrapper for the Lastz alignment tool on paired reads | -- | - | To update | -- | Next Gen Mappers | -lastz_paired_reads | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads | -
- | lda_analysis | -1.0.1 | -- | R | -To update | -- | - | - | - | Perform Linear Discriminant Analysis | -- | - | To update | -- | Graphics, Statistics | -lda_analysis | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis | -
- | linear_regression | -1.0.1 | -- | R | -To update | -- | - | - | - | Perform Linear Regression | -- | - | To update | -- | Statistics | -linear_regression | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression | -
- | logistic_regression_vif | -1.0.1 | -- | numpy | -To update | -- | - | - | - | Perform Logistic Regression with vif | -- | - | To update | -- | Sequence Analysis, Variant Analysis, Statistics | -logistic_regression_vif | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif | -
- | maf_cpg_filter | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Mask CpG/non-CpG sites from MAF file | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -maf_cpg_filter | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter | -
- | mapping_to_ucsc | -1.0.0 | -- | - | To update | -- | - | - | - | Format mapping data as UCSC custom track | -- | - | To update | -- | Visualization, Convert Formats, Next Gen Mappers | -mapping_to_ucsc | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc | -
- | megablast_xml_parser | -1.0.1 | -- | python | -To update | -- | - | - | - | Parse blast XML output | -- | - | To update | -- | Next Gen Mappers, Convert Formats | -megablast_xml_parser | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser | -
- | merge_cols | -1.0.3 | -- | python | -To update | -- | - | - | - | Merge columns together. | -- | - | To update | -- | Text Manipulation | -merge_cols | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols | -
- | microsatellite_birthdeath | -1.0.0 | -- | - | To update | -- | - | - | - | Identify microsatellite births and deaths | -- | - | To update | -- | Sequence Analysis | -microsatellite_birthdeath | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath | -
- | microsats_alignment_level | -1.0.0 | -- | sputnik | -To update | -- | - | - | - | Extract Orthologous Microsatellites from pair-wise alignments | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -microsats_alignment_level | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level | -
- | microsats_mutability | -1.1.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Estimate microsatellite mutability by specified attributes | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -microsats_mutability | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability | -
- | mine | -0.0.1 | -- | MINE | -To update | -- | - | - | - | Maximal Information-based Nonparametric Exploration | -- | - | To update | -- | Variant Analysis | -mine | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine | -
- | multispecies_orthologous_microsats | -1.0.0 | -- | bx-sputnik | -To update | -- | - | - | - | Extract orthologous microsatellites | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -multispecies_orthologous_microsats | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats | -
- | mutate_snp_codon | -1.0.0 | -- | - | To update | -- | - | - | - | Mutate Codons with SNPs | -- | - | To update | -- | Variant Analysis | -mutate_snp_codon | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon | -
- | partialr_square | -1.0.0 | -- | R | -To update | -- | - | - | - | Compute partial R square | -- | - | To update | -- | Statistics | -partialr_square | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square | -
- | pearson_correlation | -1.0.0 | -- | - | To update | -- | - | - | - | Pearson and apos Correlation between any two numeric columns | -- | - | To update | -- | Statistics | -pearson_correlation | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation | -
- | pgsnp2gd_snp | -1.0.0 | -- | - | To update | -- | - | - | - | Convert from pgSnp to gd_snp | -- | - | To update | -- | Variant Analysis | -pgsnp2gd_snp | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp | -
- | pileup_interval | -1.0.3 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Pileup-to-Interval condenses pileup format into ranges of bases | -- | - | To update | -- | SAM | -pileup_interval | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval | -
- | pileup_parser | -1.0.2 | -- | perl | -To update | -- | - | - | - | Filter pileup on coverage and SNPs | -- | - | To update | -https://github.com/galaxyproject/tools-devteam/ | -SAM | -pileup_parser | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser | -
- | plot_from_lda | -1.0.1 | -- | R | -To update | -- | - | - | - | Draw ROC plot on "Perform LDA" output | -- | - | To update | -- | Graphics, Statistics | -plot_from_lda | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda | -
- | principal_component_analysis | -1.0.2 | -- | rpy | -To update | -- | - | - | - | Principal Component Analysis | -- | - | To update | -- | Statistics | -principal_component_analysis | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis | -
- | quality_filter | -1.0.1 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Filter nucleotides based on quality scores | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -quality_filter | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter | -
- | rcve | -1.0.0 | -- | R | -To update | -- | - | - | - | Compute RCVE | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -rcve | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve | -
- | remove_beginning | -1.0.0 | -- | - | To update | -- | - | - | - | Remove lines from the beginning of a file. | -- | - | To update | -- | Text Manipulation | -remove_beginning | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning | -
- | rmap | -1.0.0 | -2.1 | -rmap | -To update | -- | - | - | - | RMAP for Solexa Short Reads Alignment | -- | - | To update | -- | Next Gen Mappers | -rmap | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap | -
- | rmapq | -1.0.0 | -2.1 | -rmap | -To update | -- | - | - | - | RMAPQ for Solexa Short Reads Alignment with Quality Scores | -- | - | To update | -- | Next Gen Mappers | -rmapq | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq | -
- | sam2interval | -1.0.2 | -- | python | -To update | -- | - | - | - | Convert SAM to interval. | -- | - | To update | -- | SAM | -sam2interval | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval | -
- | sam_bitwise_flag_filter | -1.0.1 | -- | python | -To update | -- | - | - | - | Filter SAM on bitwise flag values | -- | - | To update | -- | SAM | -sam_bitwise_flag_filter | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter | -
- | scatterplot | -1.0.3 | -- | numpy | -To update | -- | - | - | - | Scatterplot of two numeric columns | -- | - | To update | -- | Graphics, Statistics | -scatterplot | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot | -
- | short_reads_figure_high_quality_length | -1.0.0 | -- | rpy | -To update | -- | - | - | - | Histogram of high quality score reads | -- | - | To update | -- | Sequence Analysis, Graphics | -short_reads_figure_high_quality_length | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length | -
- | short_reads_figure_score | -1.0.2 | -- | fontconfig | -To update | -- | - | - | - | Build base quality distribution | -- | - | To update | -- | Sequence Analysis, Graphics | -short_reads_figure_score | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score | -
- | short_reads_trim_seq | -1.0.0 | -- | - | To update | -- | - | - | - | Select high quality segments | -- | - | To update | -- | Fastq Manipulation | -short_reads_trim_seq | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq | -
- | show_beginning | -1.0.0 | -- | - | To update | -- | - | - | - | Select lines from the beginning of a file. | -- | - | To update | -- | Text Manipulation | -show_beginning | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning | -
- | show_tail | -1.0.0 | -- | - | To update | -- | - | - | - | Select lines from the end of a file. | -- | - | To update | -- | Text Manipulation | -show_tail | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail | -
- | sicer | -1.1 | -1.1 | -SICER | -Up-to-date | -- | - | - | - | Statistical approach for the Identification of ChIP-Enriched Regions | -- | - | Up-to-date | -https://home.gwu.edu/~wpeng/Software.htm | -ChIP-seq | -sicer | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer | -
- | split_paired_reads | -1.0.0 | -- | - | To update | -- | - | - | - | Split paired end reads | -- | - | To update | -- | Fastq Manipulation | -split_paired_reads | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads | -
- | substitution_rates | -1.0.0 | -- | - | To update | -- | - | - | - | Estimate substitution rates for non-coding regions | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -substitution_rates | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates | -
- | substitutions | -1.0.1 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Fetch substitutions from pairwise alignments | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -substitutions | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions | -
- | t_test_two_samples | -1.0.1 | -- | R | -To update | -- | - | - | - | T Test for Two Samples | -- | - | To update | -- | Statistics | -t_test_two_samples | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples | -
- | table_annovar | -0.2 | -- | annovar | -To update | -- | - | - | - | Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered | -- | - | To update | -- | Variant Analysis | -table_annovar | -devteam | -Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar | -
- | tabular_to_fasta | -1.1.1 | -- | python | -To update | -- | - | - | - | Tabular-to-FASTA | -- | - | To update | -- | Convert Formats | -tabular_to_fasta | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta | -
- | tophat | -1.5.0 | -1.19.2 | -samtools | -To update | -- | - | - | - | Tophat for Illumina | -- | - | To update | -- | RNA, Next Gen Mappers | -tophat | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat | -
- | tophat2 | -2.1.1 | -2.5.3 | -bowtie2 | -To update | -- | - | - | - | Tophat - fast splice junction mapper for RNA-Seq reads | -- | - | To update | -http://ccb.jhu.edu/software/tophat/index.shtml | -RNA, Next Gen Mappers | -tophat2 | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 | -
- | tophat_fusion_post | -0.1 | -- | blast+ | -To update | -- | - | - | - | Wrapper for Tophat-Fusion post step | -- | - | To update | -- | Transcriptomics | -tophat_fusion_post | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post | -
- | trimmer | -0.0.1 | -- | - | To update | -- | - | - | - | Trim leading or trailing characters. | -- | - | To update | -- | Text Manipulation | -trimmer | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer | -
- | ucsc_custom_track | -1.0.1 | -- | python | -To update | -- | - | - | - | Build custom track for UCSC genome browser | -- | - | To update | -- | Sequence Analysis | -ucsc_custom_track | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track | -
- | varscan_version_2 | -2.4.2 | -2.4.6 | -varscan | -To update | -- | - | - | - | VarScan wrapper | -- | - | To update | -https://dkoboldt.github.io/varscan/ | -Variant Analysis | -varscan_version_2 | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 | -
- | vcf2pgsnp | -1.0.0 | -- | - | To update | -- | - | - | - | VCF to pgSnp | -- | - | To update | -- | Variant Analysis | -vcf2pgsnp | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp | -
- | vcf_annotate | -1.0.0 | -- | - | To update | -- | - | - | - | Annotate a VCF file (dbSNP, hapmap) | -- | - | To update | -- | Variant Analysis | -vcf_annotate | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate | -
- | vcf_extract | -1.0.0 | -- | - | To update | -- | - | - | - | Extract reads from a specified region | -- | - | To update | -- | Variant Analysis | -vcf_extract | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract | -
- | vcf_filter | -1.0.0 | -- | - | To update | -- | - | - | - | Filter a VCF file | -- | - | To update | -- | Variant Analysis | -vcf_filter | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter | -
- | vcf_intersect | -1.0.0 | -- | - | To update | -- | - | - | - | Generate the intersection of two VCF files | -- | - | To update | -- | Variant Analysis | -vcf_intersect | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect | -
- | weightedaverage | -1.0.1 | -1.1.0 | -galaxy-ops | -To update | -- | - | - | - | Assign weighted-average of the values of features overlapping an interval | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -weightedaverage | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage | -
- | windowsplitter | -1.0.1 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Make windows | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -windowsplitter | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter | -
- | xy_plot | -1.0.2 | -- | r-base | -To update | -- | - | - | - | Plotting tool for multiple series and graph types | -- | - | To update | -- | Graphics, Statistics | -xy_plot | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot | -
- | basecoverage | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Base Coverage of all intervals | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -basecoverage | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage | -
- | cluster | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Cluster the intervals of a dataset | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -cluster | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster | -
- | complement | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Complement intervals of a dataset | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -complement | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement | -
- | concat | -1.0.1 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Concatenate two bed files | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -concat | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat | -
- | coverage | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Coverage of a set of intervals on second set of intervals | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -coverage | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage | -
- | flanking_features | -4.0.1 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Fetch closest non-overlapping feature for every interval | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -flanking_features | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features | -
- | get_flanks | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Get flanks returns flanking region/s for every gene | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -get_flanks | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks | -
- | intersect | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Intersect the intervals of two datasets | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -intersect | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect | -
- | join | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Join the intervals of two datasets side-by-side | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -join | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join | -
- | merge | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Merge the overlapping intervals of a dataset | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -merge | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge | -
- | subtract | -1.0.0 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Subtract the intervals of two datasets | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -subtract | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract | -
- | subtract_query | -0.1 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Subtract Whole Dataset from another dataset | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -subtract_query | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query | -
- | tables_arithmetic_operations | -1.0.0 | -- | perl | -To update | -- | - | - | - | Arithmetic Operations on tables | -- | - | To update | -https://github.com/galaxyproject/gops | -Genomic Interval Operations | -tables_arithmetic_operations | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations | -
- | hgv_fundo | -1.0.0 | -- | - | To update | -- | - | - | - | FunDO human genes associated with disease terms | -- | - | To update | -- | Sequence Analysis | -hgv_fundo | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo | -
- | hgv_hilbertvis | -1.0.0 | -- | R | -To update | -- | - | - | - | HVIS visualization of genomic data with the Hilbert curve | -- | - | To update | -https://www.ebi.ac.uk/huber-srv/hilbert/ | -Graphics, Visualization | -hgv_hilbertvis | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis | -
- | snpfreq | -1.0.1 | -- | R | -To update | -- | - | - | - | snpFreq significant SNPs in case-control data | -- | - | To update | -- | Variant Analysis, Statistics | -snpfreq | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq | -
- | find_diag_hits | -1.0.0 | -0.10.0 | -taxonomy | -To update | -- | - | - | - | Find diagnostic hits | -- | - | To update | -https://bitbucket.org/natefoo/taxonomy | -Metagenomics | -find_diag_hits | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits | -
- | gi2taxonomy | -1.1.1 | -0.10.0 | -taxonomy | -To update | -- | - | - | - | Fetch taxonomic representation | -- | - | To update | -https://bitbucket.org/natefoo/taxonomy | -Metagenomics | -gi2taxonomy | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy | -
- | kraken2tax | -1.2+galaxy0 | -- | gawk | -To update | -- | - | - | - | Convert Kraken output to Galaxy taxonomy data. | -- | - | To update | -https://bitbucket.org/natefoo/taxonomy | -Metagenomics | -kraken2tax | -devteam | -https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ | -
- | lca_wrapper | -1.0.1 | -0.10.0 | -taxonomy | -To update | -- | - | - | - | Find lowest diagnostic rank | -- | - | To update | -https://bitbucket.org/natefoo/taxonomy | -Metagenomics | -lca_wrapper | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper | -
- | poisson2test | -1.0.0 | -0.10.0 | -taxonomy | -To update | -- | - | - | - | Poisson two-sample test | -- | - | To update | -https://bitbucket.org/natefoo/taxonomy | -Statistics, Metagenomics | -poisson2test | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test | -
- | t2ps | -1.0.0 | -0.10.0 | -taxonomy | -To update | -- | - | - | - | Draw phylogeny | -- | - | To update | -https://bitbucket.org/natefoo/taxonomy | -Metagenomics | -t2ps | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps | -
- | t2t_report | -1.0.0 | -0.10.0 | -taxonomy | -To update | -- | - | - | - | Summarize taxonomy | -- | - | To update | -https://bitbucket.org/natefoo/taxonomy | -Metagenomics | -t2t_report | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report | -
- | vcftools_annotate | -0.1 | -- | echo | -To update | -- | - | - | - | Annotate VCF using custom/user-defined annotations | -- | - | To update | -https://vcftools.github.io/ | -Variant Analysis | -vcftools_annotate | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate | -
- | vcftools_compare | -0.1 | -1.11 | -tabix | -To update | -- | - | - | - | Compare VCF files to get overlap and uniqueness statistics | -- | - | To update | -https://vcftools.github.io/ | -Variant Analysis | -vcftools_compare | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare | -
- | vcftools_consensus | -0.1.11 | -1.19.2 | -samtools | -To update | -- | - | - | - | Apply VCF variants to a fasta file to create consensus sequence | -- | - | To update | -https://vcftools.github.io/ | -Variant Analysis | -vcftools_consensus | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus | -
- | vcftools_isec | -0.1.1 | -1.11 | -tabix | -To update | -- | - | - | - | Intersect multiple VCF datasets | -- | - | To update | -https://vcftools.github.io/ | -Variant Analysis | -vcftools_isec | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec | -
- | vcftools_merge | -0.1.11 | -1.11 | -tabix | -To update | -- | - | - | - | Merge multiple VCF datasets into a single dataset | -- | - | To update | -https://vcftools.github.io/ | -Variant Analysis | -vcftools_merge | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge | -
- | vcftools_slice | -0.1 | -- | echo | -To update | -- | - | - | - | Subset VCF dataset by genomic regions | -- | - | To update | -https://vcftools.github.io/ | -Variant Analysis | -vcftools_slice | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice | -
- | vcftools_subset | -0.1 | -1.11 | -tabix | -To update | -- | - | - | - | Select samples from a VCF dataset | -- | - | To update | -https://vcftools.github.io/ | -Variant Analysis | -vcftools_subset | -devteam | -https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset | -
- | 10x_bamtofastq | -1.4.1 | -1.4.1 | -10x_bamtofastq | -Up-to-date | -- | - | - | - | Converts 10x Genomics BAM to FASTQ | -- | - | Up-to-date | -https://github.com/10XGenomics/bamtofastq | -Convert Formats | -10x_bamtofastq | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq | -
- | AggregateAlignments | -0.6.0 | -0.6.0 | -graphclust-wrappers | -Up-to-date | -- | - | - | - | Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. | -- | - | Up-to-date | -- | RNA | -graphclust_aggregate_alignments | -rnateam | -https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments | -
- | AlignCluster | -0.1 | -0.6.0 | -graphclust-wrappers | -To update | -- | - | - | - | Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. | -- | - | To update | -- | RNA | -graphclust_align_cluster | -rnateam | -https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster | -
- | CMFinder | -0.4 | -0.6.0 | -graphclust-wrappers | -To update | -- | - | - | - | Determines consensus motives for sequences. | -- | - | To update | -- | RNA | -graphclust_cmfinder | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder | -
- | CollectResults | -0.5 | -0.6.0 | -graphclust-wrappers | -To update | -- | - | - | - | Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. | -- | - | To update | -- | RNA | -graphclust_postprocessing | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults | -
- | CollectResultsNoAlign | -0.5 | -0.6.0 | -graphclust-wrappers | -To update | -- | - | - | - | Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. | -- | - | To update | -- | RNA | -graphclust_postprocessing_no_align | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign | -
- | GSPAN | -0.4 | -0.6.0 | -graphclust-wrappers | -To update | -- | - | - | - | Second step of GraphClust | -- | - | To update | -- | RNA | -graphclust_fasta_to_gspan | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN | -
- | LocARNAGraphClust | -0.4 | -0.6.0 | -graphclust-wrappers | -To update | -- | - | - | - | MLocARNA computes a multiple sequence-structure alignment of RNA sequences. | -- | - | To update | -- | RNA | -graphclust_mlocarna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust | -
- | NSPDK | -9.2.3.1 | -0.6.0 | -graphclust-wrappers | -To update | -- | - | - | - | Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. | -- | - | To update | -- | RNA | -graphclust_nspdk | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK | -
- | Plotting | -0.4 | -- | seaborn | -To update | -- | - | - | - | Plotting results for GraphClust | -- | - | To update | -- | RNA | -graphclust_motif_finder_plot | -rnateam | -https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting | -
- | PrepareForMlocarna | -0.4 | -0.6.0 | -graphclust-wrappers | -To update | -- | - | - | - | This tool prepares files for locarna step. | -- | - | To update | -- | RNA | -graphclust_prepocessing_for_mlocarna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna | -
- | Preprocessing | -0.5 | -0.6.0 | -graphclust-wrappers | -To update | -- | - | - | - | Preprocessing input for GraphClust | -- | - | To update | -- | RNA | -graphclust_preprocessing | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust | -
- | Structure_GSPAN | -0.4 | -0.6.0 | -graphclust-wrappers | -To update | -- | - | - | - | Convert RNA structure to GSPAN graphs | -- | - | To update | -- | RNA | -structure_to_gspan | -rnateam | -https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN | -
- | agat | -1.2.0 | -1.3.0 | -agat | -To update | -agat | -AGAT | -Data handling, Genome annotation | -Genomics | -GTF/GFF analysis toolkit | -Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. | -- | To update | -https://github.com/NBISweden/AGAT | -Convert Formats, Statistics, Fasta Manipulation | -agat | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/agat | -
- | antismash | -6.1.1 | -7.1.0 | -antismash | -To update | -antismash | -antiSMASH | -Sequence clustering, Gene prediction, Differential gene expression analysis | -Molecular interactions, pathways and networks, Gene and protein families | -Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters | -Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. | -- | To update | -https://antismash.secondarymetabolites.org | -Sequence Analysis | -antismash | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash | -
- | atactk_trim_adapters | -0.1.6 | -0.1.9 | -atactk | -To update | -- | - | - | - | Trim adapters from paired-end HTS reads. | -- | - | To update | -https://github.com/ParkerLab/atactk/ | -Fastq Manipulation | -atactk_trim_adapters | -rnateam | -https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters | -
- | augustus | -3.1.0 | -3.5.0 | -augustus | -To update | -- | - | - | - | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. | -- | - | To update | -http://bioinf.uni-greifswald.de/augustus/ | -Sequence Analysis | -augustus | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/augustus | -
- | bamhash | -1.1 | -1.1 | -bamhash | -Up-to-date | -- | - | - | - | Hash BAM and FASTQ files to verify data integrity | -- | - | Up-to-date | -https://github.com/DecodeGenetics/BamHash | -Sequence Analysis | -bamhash | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/bamhash | -
- | barcode_collapse | -0.1.0 | -0.22.0 | -pysam | -To update | -- | - | - | - | Paired End randomer aware duplicate removal algorithm | -- | - | To update | -https://github.com/YeoLab/gscripts | -RNA, Sequence Analysis | -barcode_collapse | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse | -
- | bigwig_to_bedgraph | -0.1.0 | -- | ucsc_tools | -To update | -- | - | - | - | Convert from bigWig to bedGraph format | -- | - | To update | -- | Convert Formats | -bigwig_to_bedgraph | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph | -
- | biomodelsML | -1 | -- | - | To update | -- | - | - | - | Random Forest model to predict efficacy of immune checkpoint blockade across multiple cancer patient cohorts | -- | - | To update | -https://www.ebi.ac.uk/biomodels/BIOMD0000001066 | -Machine Learning | -biomodels_biomd0000001066 | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML | -
- | bionano | -3.7.0 | -- | - | To update | -- | - | - | - | Bionano Solve is a set of tools for analyzing Bionano data | -- | - | To update | -https://bionanogenomics.com/ | -Assembly | -bionano | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/bionano | -
- | bismark | -0.22.1 | -0.24.2 | -bismark | -To update | -- | - | - | - | A tool to map bisulfite converted sequence reads and determine cytosine methylation states | -- | - | To update | -https://www.bioinformatics.babraham.ac.uk/projects/bismark/ | -Sequence Analysis, Next Gen Mappers | -bismark | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/bismark | -
- | blobtoolkit | -4.0.7 | -- | - | To update | -- | - | - | - | Identification and isolation non-target data in draft and publicly available genome assemblies. | -- | - | To update | -https://blobtoolkit.genomehubs.org/ | -Sequence Analysis, Assembly | -blobtoolkit | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit | -
- | blockbuster | -0.1.2 | -0.0.1.1 | -blockbuster | -To update | -- | - | - | - | Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. | -- | - | To update | -http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html | -RNA, Sequence Analysis | -blockbuster | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster | -
- | canu | -2.2 | -2.2 | -canu | -Up-to-date | -canu | -CANU | -De-novo assembly | -Genomics | -Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). | -De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. | -- | Up-to-date | -https://github.com/marbl/canu | -- | canu | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/canu | -
- | cellpose | -3.0.1 | -- | - | To update | -- | - | - | - | Cellpose is an anatomical segmentation algorithm | -- | - | To update | -https://github.com/MouseLand/cellpose | -Imaging | -cellpose | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/cellpose | -
- | cellprofiler | -- | - | - | To update | -CellProfiler | -CellProfiler | -Quantification, Image analysis, Parsing | -Imaging, Microarray experiment, Genotype and phenotype | -cellProfiler wrapper | -Tool for quantifying data from biological images, particularly in high-throughput experiments. | -cellprofiler | -To update | -- | Imaging | -cellprofiler | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools | -
- | cellprofiler_v4 | -4.2.6 | -- | - | To update | -- | - | - | - | cellProfiler4 wrapper | -- | - | To update | -- | Imaging | -cellprofiler4 | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools | -
- | chipseeker | -1.32.0 | -1.38.0 | -bioconductor-chipseeker | -To update | -- | - | - | - | A tool for ChIP peak annotation and visualization | -- | - | To update | -https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html | -ChIP-seq, Genome annotation | -chipseeker | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker | -
- | circexplorer | -1.1.9.0 | -1.1.10 | -circexplorer | -To update | -- | - | - | - | A combined strategy to identify circular RNAs (circRNAs and ciRNAs) | -- | - | To update | -https://github.com/YangLab/CIRCexplorer | -Sequence Analysis, RNA | -circexplorer | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer | -
- | combine_metaphlan_humann | -0.3.0 | -- | python | -To update | -combine_metaphlan_and_humann | -Combine Metaphlan and HUMAnN | -Aggregation | -Metagenomics, Molecular interactions, pathways and networks | -Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances | -"This tool combine MetaPhlAn outputs and HUMANnN outputs." - Galaxy tool wrapper | -- | To update | -- | Metagenomics | -combine_metaphlan2_humann2 | -bebatut | -https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 | -
- | compare_humann2_output | -0.2.0 | -- | - | To update | -compare_humann2_outputs | -Compare HUMAnN2 outputs | -Comparison | -Metagenomics, Gene and protein families | -Compare outputs of HUMAnN2 for several samples and extract similar and specific information | -"This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples." - Galaxy tool wrapper | -- | To update | -- | Metagenomics | -compare_humann2_output | -bebatut | -https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output | -
- | cpat | -3.0.5 | -3.0.5 | -cpat | -Up-to-date | -- | - | - | - | Coding-potential assessment tool using an alignment-free logistic regression model. | -- | - | Up-to-date | -https://github.com/liguowang/cpat | -Transcriptomics | -cpat | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/cpat | -
- | crt | -1.2.0 | -1.2 | -crisper_recognition_tool | -To update | -- | - | - | - | CRISPR Recognition Tool | -- | - | To update | -- | Sequence Analysis | -crispr_recognition_tool | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/crt | -
- | diff | -3.7 | -- | diffutils | -To update | -- | - | - | - | GNU diff tool that calculates the differences between two files. | -- | - | To update | -http://www.gnu.org/software/diffutils/ | -Text Manipulation | -diff | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/diff | -
- | diffbind | -- | - | - | To update | -- | - | - | - | Diffbind provides functions for processing ChIP-Seq data. | -- | - | To update | -http://bioconductor.org/packages/release/bioc/html/DiffBind.html | -ChIP-seq | -diffbind | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/diffbind | -
- | edta | -- | 2.2.0 | -edta | -To update | -edta | -The Extensive de novo TE Annotator (EDTA) | -De-novo assembly, Deisotoping, Genome annotation | -Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms | -The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. | -The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. | -- | To update | -https://github.com/oushujun/EDTA | -Variant Analysis | -edta | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta | -
- | epicseg | -@VERSION_STRING@ | -1.0 | -epicseg | -To update | -- | - | - | - | EpiCSeg is a tool for conducting chromatin segmentation. | -- | - | To update | -https://github.com/lamortenera/epicseg | -Epigenetics | -epicseg | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/epicseg | -
- | fastq_info | -0.25.1 | -0.25.2 | -fastq_utils | -To update | -- | - | - | - | FASTQ info allows to validate single or paired fastq files | -- | - | To update | -https://github.com/nunofonseca/fastq_utils | -Fastq Manipulation | -fastq_info | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info | -
- | file_manipulation | -0.4 | -- | python | -To update | -- | - | - | - | This tool returns all unique lines from a tab-separated file. | -- | - | To update | -https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation | -Text Manipulation | -unique | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation | -
- | find_subsequences | -0.3 | -1.70 | -biopython | -To update | -- | - | - | - | - | - | - | To update | -- | - | find_subsequences | -bgruening | -- |
- | flye | -2.9.3 | -2.9.3 | -flye | -Up-to-date | -- | - | - | - | Assembly of long and error-prone reads. | -- | - | Up-to-date | -https://github.com/fenderglass/Flye/ | -Assembly | -flye | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/flye | -
- | footprint | -1.0.0 | -1.0.1 | -footprint | -To update | -- | - | - | - | Find transcription factor footprints | -- | - | To update | -https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ | -Epigenetics | -footprint | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/footprint | -
- | format_cd_hit_output | -1.0.0+galaxy1 | -- | - | To update | -- | - | - | - | Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file | -- | - | To update | -- | Fasta Manipulation | -format_cd_hit_output | -bebatut | -https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ | -
- | format_metaphlan2_output | -0.2.0 | -- | - | To update | -format_metaphlan2_output | -Format metaphlan2 output | -Formatting | -Taxonomy, Metagenomics | -Format MetaPhlAn2 output to extract abundance at different taxonomic levels | -"This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains)." - Galaxy tool wrapper | -- | To update | -- | Metagenomics | -format_metaphlan2_output | -bebatut | -https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ | -
- | gfastats | -1.3.6 | -1.3.6 | -gfastats | -Up-to-date | -gfastats | -gfastats | -Data handling | -Computational biology | -Tool for generating sequence statistics and simultaneous genome assembly file manipulation. | -gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. | -- | Up-to-date | -https://github.com/vgl-hub/gfastats | -Sequence Analysis | -gfastats | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/gfastats | -
- | glimmer_hmm | -- | - | - | To update | -- | - | - | - | GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) | -- | - | To update | -https://ccb.jhu.edu/software/glimmerhmm/ | -Sequence Analysis | -glimmer_hmm | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm | -
- | gotohscan | -1.3.0 | -1.3 | -gotohscan | -To update | -- | - | - | - | Find subsequences in db | -- | - | To update | -- | Sequence Analysis | -gotohscan | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan | -
- | graph_converter | -0.1.0 | -- | - | To update | -- | - | - | - | Convert between different graph formats | -- | - | To update | -- | Convert Formats | -graph_converter | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter | -
- | graphclust | -0.1 | -- | GraphClust | -To update | -- | - | - | - | GraphClust can be used for structural clustering of RNA sequences. | -- | - | To update | -http://www.bioinf.uni-freiburg.de/Software/GraphClust/ | -RNA | -graphclust | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/graphclust | -
- | graphmap | -0.5.2 | -0.6.3 | -graphmap | -To update | -- | - | - | - | Mapper for long, error-prone reads. | -- | - | To update | -https://github.com/isovic/graphmap/ | -Assembly | -graphmap | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/graphmap | -
- | hclust2 | -0.99 | -1.0.0 | -hclust2 | -To update | -- | - | - | - | Plots heatmaps | -- | - | To update | -https://bitbucket.org/nsegata/hclust2/ | -Data Visualization | -hclust2 | -rnateam | -https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 | -
- | hictk | -0.0.8 | -0.0.9 | -hictk | -To update | -- | - | - | - | hictk, a blazing-fast toolkit to work with .hic and .cool files | -- | - | To update | -https://github.com/paulsengroup/hictk | -- | hictk | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/hictk | -
- | hicup | -0.9.2 | -- | - | To update | -- | - | - | - | The HiCUP-Pipeline from the Bioinformatics Babraham Institute. | -- | - | To update | -https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html | -Epigenetics | -hicup | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/hicup | -
- | hifiasm | -0.19.8 | -0.19.8 | -hifiasm | -Up-to-date | -- | - | - | - | A fast haplotype-resolved de novo assembler | -- | - | Up-to-date | -https://github.com/chhylp123/hifiasm | -Assembly | -hifiasm | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm | -
- | homer | -- | - | - | To update | -- | - | - | - | Software for motif discovery and next generation sequencing analysis. | -- | - | To update | -http://homer.salk.edu/homer/ | -Sequence Analysis | -homer | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/homer | -
- | illumina_methylation_analyser | -0.1 | -- | Rscript | -To update | -- | - | - | - | Methylation analyzer for Illumina 450k DNA emthylation microarrays | -- | - | To update | -https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser | -Sequence Analysis | -illumina_methylation_analyser | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser | -
- | bia-ftplinks | -0.1.0 | -- | wget | -To update | -- | - | - | - | Tool to query ftp links for study from bioimage archive | -- | - | To update | -- | Imaging | -bia_download | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools | -
- | graphicsmagick | -1.3.42 | -1.3.26 | -graphicsmagick | -To update | -- | - | - | - | Contains tools based on GraphicsMagick | -- | - | To update | -http://www.graphicsmagick.org | -Imaging | -graphicsmagick | -bgruening | -https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ | -
- | imagej2 | -- | - | - | To update | -imagej | -ImageJ2 | -Image analysis, Image annotation, Visualisation | -Imaging | -ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. | -It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. | -imagej2 | -To update | -http://fiji.sc | -Imaging | -imagej2 | -imgteam | -https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 | -
- | woundhealing | -1.6.1 | -1.6.1 | -fiji-morpholibj | -Up-to-date | -- | - | - | - | Tool to automate quantification of wound healing in high-throughput microscopy scratch assays | -- | - | Up-to-date | -https://git.embl.de/grp-cba/wound-healing-htm-screen | -Imaging | -Wound healing scratch assay image analysis | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools | -
- | instagraal | -0.1.6 | -- | - | To update | -instagraal | -instaGRAAL | -Genome assembly, Mapping assembly, Genetic mapping, Scaffolding | -Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites | -Large genome reassembly based on Hi-C data | -Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) | -- | To update | -https://github.com/koszullab/instaGRAAL | -Assembly | -instagraal | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/instagraal | -
- | iprscan5 | -- | - | - | To update | -- | - | - | - | Interproscan queries the interpro database and provides annotations. | -- | - | To update | -http://www.ebi.ac.uk/Tools/pfa/iprscan5/ | -Sequence Analysis | -iprscan5 | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 | -
- | itsx | -1.1.3 | -1.1.3 | -itsx | -Up-to-date | -ITSx | -ITSx | -Sequence feature detection | -Functional, regulatory and non-coding RNA, Microbiology | -ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. | -TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. | -- | Up-to-date | -https://microbiology.se/software/itsx/ | -Metagenomics | -itsx | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/itsx | -
- | jupyter_job | -0.0.1 | -- | - | To update | -- | - | - | - | Run jupyter notebook script in Galaxy | -- | - | To update | -- | Machine Learning | -run_jupyter_job | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job | -
- | labels | -1.0.5.0 | -- | labels | -To update | -- | - | - | - | remaps and annotates alignments | -- | - | To update | -https://github.com/bgruening/galaxytools/tree/master/tools/labels | -Sequence Analysis | -labels | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/labels | -
- | lighter | -1.0 | -1.1.2 | -lighter | -To update | -- | - | - | - | Lighter is a kmer-based error correction method for whole genome sequencing data | -- | - | To update | -- | Sequence Analysis, Fasta Manipulation | -lighter | -bgruening | -https://github.com/mourisl/Lighter | -
- | mafft | -7.508 | -7.520 | -mafft | -To update | -MAFFT | -MAFFT | -Multiple sequence alignment | -Sequence analysis | -Multiple alignment program for amino acid or nucleotide sequences | -MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. | -- | To update | -- | RNA | -mafft | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/mafft | -
- | mavedb | -0.9 | -- | - | To update | -- | - | - | - | data source for MaveDB | -- | - | To update | -- | Data Source | -mavedb_importer | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ | -
- | mcl | -14.137 | -22.282 | -mcl | -To update | -- | - | - | - | Markov Cluster Algorithm | -- | - | To update | -http://micans.org/mcl/ | -Sequence Analysis, Metagenomics | -mcl | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/mcl | -
- | methtools | -0.1.1 | -- | methtools | -To update | -- | - | - | - | tools for methylation analysis | -- | - | To update | -https://github.com/bgruening/galaxytools/tree/master/tools/methtools | -Sequence Analysis | -methtools | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/methtools | -
- | methyldackel | -0.5.2 | -0.6.1 | -methyldackel | -To update | -- | - | - | - | A tool for processing bisulfite sequencing alignments | -- | - | To update | -https://github.com/dpryan79/MethylDackel | -Sequence Analysis | -pileometh | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel | -
- | methylkit | -0.99.2 | -1.28.0 | -bioconductor-methylkit | -To update | -- | - | - | - | A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. | -- | - | To update | -http://bioconductor.org/packages/release/bioc/html/methylKit.html | -Epigenetics | -methylkit | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/methylkit | -
- | metilene | -0.2.6.1 | -0.2.8 | -metilene | -To update | -- | - | - | - | Differential DNA methylation calling | -- | - | To update | -- | RNA, Statistics | -metilene | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/metilene | -
- | miclip | -1.2.0 | -- | Rscript | -To update | -- | - | - | - | Identification of binding sites in CLIP-Seq data. | -- | - | To update | -https://cran.r-project.org/src/contrib/Archive/MiClip/ | -Sequence Analysis | -miclip | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/miclip | -
- | minced | -0.2.0 | -0.4.2 | -minced | -To update | -- | - | - | - | MinCED - Mining CRISPRs in Environmental Datasets | -- | - | To update | -http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README | -Sequence Analysis | -minced | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/minced | -
- | minipolish | -0.1.3 | -0.1.3 | -minipolish | -Up-to-date | -minipolish | -minipolish | -Localised reassembly, Read depth analysis | -Sequence assembly, Sequencing | -Polishing miniasm assemblies | -A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. | -- | Up-to-date | -https://github.com/rrwick/Minipolish | -Sequence Analysis | -minipolish | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/minipolish | -
- | mitohifi | -3 | -- | - | To update | -- | - | - | - | Assembly mitogenomes from Pacbio HiFi read. | -- | - | To update | -https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 | -Assembly | -mitohifi | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi | -
- | molecule2gspan | -0.2 | -2.3.90dev7d621d9 | -openbabel | -To update | -- | - | - | - | converter | -- | - | To update | -https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan | -Convert Formats | -molecule_to_gspan | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan | -
- | music_deconvolution | -0.1.1 | -0.1.1 | -music-deconvolution | -Up-to-date | -- | - | - | - | Multi-subject Single Cell deconvolution (MuSiC) | -- | - | Up-to-date | -https://github.com/xuranw/MuSiC | -Transcriptomics | -music | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ | -
- | nanopolish | -0.14.0 | -0.14.0 | -nanopolish | -Up-to-date | -- | - | - | - | Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. | -- | - | Up-to-date | -https://github.com/jts/nanopolish | -- | nanopolish | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish | -
- | netboxr | -1.6.0 | -1.9.0 | -bioconductor-netboxr | -To update | -- | - | - | - | netboxr enables automated discovery of biological process modules by network analysis | -- | - | To update | -- | Systems Biology | -netboxr | -bgruening | -- |
- | nextdenovo | -2.5.0 | -2.5.2 | -nextdenovo | -To update | -nextdenovo | -NextDenovo | -De-novo assembly, Genome assembly | -Sequencing, Sequence assembly | -String graph-based de novo assembler for long reads | -NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. | -- | To update | -https://github.com/Nextomics/NextDenovo | -Assembly | -nextdenovo | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo | -
- | nucleosome_prediction | -3.0 | -3.0 | -nucleosome_prediction | -Up-to-date | -- | - | - | - | Prediction of Nucleosomes Positions on the Genome | -- | - | Up-to-date | -https://genie.weizmann.ac.il/software/nucleo_exe.html | -Sequence Analysis | -nucleosome_prediction | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction | -
- | numeric_clustering | -0.9 | -- | anaconda | -To update | -- | - | - | - | Clustering tool for numberic values | -- | - | To update | -http://scikit-learn.org/stable/index.html | -Statistics | -numeric_clustering | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering | -
- | openms | -2.1.0 | -3.1.0 | -openms | -To update | -- | - | - | - | OpenMS in version 2.1. | -- | - | To update | -- | Proteomics | -openms | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/openms | -
- | pandas_rolling_window | -0.1 | -- | numpy | -To update | -- | - | - | - | Rolling window calculations | -- | - | To update | -https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html | -Statistics | -pandas_rolling_window | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window | -
- | peakachu | -0.2.0+galaxy1 | -0.2.0 | -peakachu | -To update | -- | - | - | - | PEAKachu is a peak-caller for CLIP- and RIP-Seq data | -- | - | To update | -- | Sequence Analysis, RNA | -peakachu | -rnateam | -https://github.com/tbischler/PEAKachu | -
- | perf | -5.11.0 | -- | perf | -To update | -- | - | - | - | suitable for boolean classification problems | -- | - | To update | -http://osmot.cs.cornell.edu/kddcup/software.html | -- | stats_perf_tool | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/perf | -
- | pfamscan | -1.6 | -1.6 | -pfam_scan | -Up-to-date | -pfamscan | -PfamScan | -Protein sequence analysis | -Sequence analysis | -Search a FASTA sequence against a library of Pfam HMM. | -This tool is used to search a FASTA sequence against a library of Pfam HMM. | -- | Up-to-date | -http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ | -Sequence Analysis | -pfamscan | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan | -
- | pg_tools | -- | - | postgresql | -To update | -- | - | - | - | tool suite for dealing with Postgresql databases from Galaxy's history | -- | - | To update | -https://www.postgresql.org | -Data Export, Data Source | -pgtools | -bgruening | -https://github.com/bgruening/galaxytools/tools/pgtools | -
- | pharmcat | -- | - | - | To update | -- | - | - | - | Pharmacogenomics Clinical Annotation Tool | -- | - | To update | -https://pharmcat.org/ | -Variant Analysis | -pharmcat | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat | -
- | piranha | -1.2.1.0 | -1.2.1 | -piranha | -To update | -- | - | - | - | Piranha is a peak-caller for CLIP- and RIP-Seq data | -- | - | To update | -- | Sequence Analysis, RNA | -piranha | -rnateam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha | -
- | platypus | -0.0.11 | -- | platypus | -To update | -- | - | - | - | efficient and accurate variant-detection in high-throughput sequencing data | -- | - | To update | -http://www.well.ox.ac.uk/platypus | -Sequence Analysis | -platypus | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/platypus | -
- | plotly_ml_performance_plots | -0.2 | -- | pandas | -To update | -- | - | - | - | performance plots for machine learning problems | -- | - | To update | -http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics | -Visualization | -plotly_ml_performance_plots | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots | -
- | plotly_parallel_coordinates_plot | -0.2 | -- | python | -To update | -- | - | - | - | parallel coordinates plot produced with plotly | -- | - | To update | -https://plot.ly/python/parallel-coordinates-plot/ | -Visualization | -plotly_parallel_coordinates_plot | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot | -
- | plotly_regression_performance_plots | -0.1 | -- | python | -To update | -- | - | - | - | performance plots for regression problems | -- | - | To update | -http://scikit-learn.org/stable/supervised_learning.html#supervised-learning | -Visualization | -plotly_regression_performance_plots | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots | -
- | protease_prediction | -0.9 | -2.0 | -eden | -To update | -- | - | - | - | This tool can learn the cleavage specificity of a given class of proteases. | -- | - | To update | -https://github.com/fabriziocosta/eden | -Sequence Analysis, Proteomics | -protease_prediction | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction | -
- | protein_properties | -0.2.0 | -1.70 | -biopython | -To update | -- | - | - | - | Calculation of various properties from given protein sequences | -- | - | To update | -- | Sequence Analysis | -protein_properties | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties | -
- | improviser | -1.1.0.1 | -- | - | To update | -- | - | - | - | Visualisation of PepXML files | -- | - | To update | -http://www.improviser.uni-freiburg.de/ | -Proteomics | -proteomics_improviser | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser | -
- | racon | -1.5.0 | -1.5.0 | -racon | -Up-to-date | -Racon | -Racon | -Genome assembly, Mapping assembly, Sequence trimming | -Whole genome sequencing, Sequence assembly, Plant biology | -Consensus module for raw de novo DNA assembly of long uncorrected reads. | -The Possibility to Use Oxford Nanopore Technology | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here: https://github.com/isovic/racon| Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step | Consensus module for raw de novo DNA assembly of long uncorrected reads | -- | Up-to-date | -https://github.com/isovic/racon | -Sequence Analysis | -racon | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/racon | -
- | repeat_masker | -0.1.2 | -4.1.5 | -RepeatMasker | -To update | -- | - | - | - | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | -- | - | To update | -http://www.repeatmasker.org/ | -Sequence Analysis | -repeat_masker | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker | -
- | replaceColumn | -0.2 | -- | - | To update | -- | - | - | - | A tool to replace all column entries of a file given by values of a key-value file. | -- | - | To update | -- | Text Manipulation | -replace_column_by_key_value_file | -bgruening | -https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn | -
- | rest_tool | -0.1.0 | -- | - | To update | -- | - | - | - | This tool fetches data from pubchem via the PubChem REST API. | -- | - | To update | -https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html | -Data Source | -pubchem_rest_tool | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool | -
- | antarna | -1.1 | -2.0.1.2 | -antarna | -To update | -- | - | - | - | antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . | -- | - | To update | -- | RNA | -antarna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ | -
- | aresite2 | -0.1.2 | -- | python | -To update | -- | - | - | - | AREsite2 REST Interface | -- | - | To update | -http://rna.tbi.univie.ac.at/AREsite | -RNA, Data Source, Sequence Analysis | -aresite2 | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 | -
- | blockclust | -1.1.1 | -1.1.1 | -blockclust | -Up-to-date | -- | - | - | - | BlockClust detects transcripts with similar processing patterns. | -- | - | Up-to-date | -https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust | -RNA | -blockclust | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust | -
- | cmsearch_deoverlap | -0.08+galaxy0 | -- | perl | -To update | -- | - | - | - | removes lower scoring overlaps from cmsearch results. | -- | - | To update | -https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl | -RNA | -cmsearch_deoverlap | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap | -
- | cmv | -1.0.8 | -1.0.8 | -cmv | -Up-to-date | -- | - | - | - | cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. | -- | - | Up-to-date | -https://github.com/eggzilla/cmv | -RNA | -cmv | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv | -
- | cofold | -2.0.4.0 | -2.0.4 | -cofold | -To update | -- | - | - | - | Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. | -- | - | To update | -http://www.e-rna.org/cofold/ | -RNA | -cofold | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold | -
- | compalignp | -1.0 | -1.0 | -compalignp | -Up-to-date | -- | - | - | - | Compute fractional identity between trusted alignment and test alignment | -- | - | Up-to-date | -- | RNA, Sequence Analysis | -compalignp | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ | -
- | coprarna | -2.1.1 | -2.1.4 | -coprarna | -To update | -- | - | - | - | Target prediction for prokaryotic trans-acting small RNAs | -- | - | To update | -https://github.com/PatrickRWright/CopraRNA | -RNA, Sequence Analysis | -coprarna | -rnateam | -https://github.com/PatrickRWright/CopraRNA | -
- | dewseq | -0.1.0+galaxy0 | -- | python | -To update | -- | - | - | - | DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data | -- | - | To update | -https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers | -Sequence Analysis, RNA, CLIP-seq | -dewseq | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq | -
- | dorina | -1.0 | -- | - | To update | -- | - | - | - | data source for RNA interactions in post-transcriptional regulation | -- | - | To update | -- | RNA, Data Source | -dorina | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ | -
- | dot2ct | -5.7.a | -6.4 | -rnastructure | -To update | -- | - | - | - | Dot-Bracket to Connect Table (CT) | -- | - | To update | -- | Sequence Analysis, RNA | -dot2ct | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct | -
- | dotknot | -1.3.1 | -- | vienna_rna | -To update | -- | - | - | - | DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence | -- | - | To update | -http://dotknot.csse.uwa.edu.au/ | -RNA, Proteomics | -dotknot | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot | -
- | exparna | -1.0.1 | -1.0.1 | -exparna | -Up-to-date | -- | - | - | - | ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. | -- | - | Up-to-date | -http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp | -RNA | -exparna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna | -
- | graphprot | -1.1.7+galaxy1 | -1.1.7 | -graphprot | -To update | -- | - | - | - | GraphProt models binding preferences of RNA-binding proteins. | -- | - | To update | -https://github.com/dmaticzka/GraphProt | -Sequence Analysis, RNA, CLIP-seq | -graphprot | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot | -
- | htseq-clip | -0.1.0+galaxy0 | -2.19.0b0 | -htseq-clip | -To update | -- | - | - | - | htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets | -- | - | To update | -https://github.com/EMBL-Hentze-group/htseq-clip | -Sequence Analysis, RNA, CLIP-seq | -htseq_clip | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip | -
- | infernal | -1.1.4 | -1.1.5 | -infernal | -To update | -infernal | -Infernal | -Nucleic acid feature detection | -Sequence sites, features and motifs | -Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. | -Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. | -- | To update | -http://infernal.janelia.org/ | -RNA | -infernal | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/infernal | -
- | inforna | -- | - | - | To update | -- | - | - | - | INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. | -- | - | To update | -http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp | -RNA | -inforna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna | -
- | intarna | -3.4.0 | -3.4.0 | -intarna | -Up-to-date | -- | - | - | - | Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. | -- | - | Up-to-date | -https://github.com/BackofenLab/IntaRNA | -RNA | -intarna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna | -
- | kinwalker | -- | - | - | To update | -- | - | - | - | Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. | -- | - | To update | -http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ | -RNA | -kinwalker | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker | -
- | locarna | -1.9.2.3 | -2.0.0 | -locarna | -To update | -- | - | - | - | LocARNA - A suite for multiple alignment and folding of RNAs | -- | - | To update | -http://www.bioinf.uni-freiburg.de/Software/LocARNA/ | -RNA | -locarna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna | -
- | mea | -0.6.4.1 | -0.6.4 | -mea | -To update | -- | - | - | - | Maximum expected accuracy prediction | -- | - | To update | -http://www.bioinf.uni-leipzig.de/Software/mea | -RNA | -mea | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea | -
- | mqc | -1.9 | -1.10 | -mqc | -To update | -- | - | - | - | Ribosome profiling mapping quality control tool | -- | - | To update | -https://github.com/Biobix/mQC | -Sequence Analysis | -mqc | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ | -
- | nastiseq | -1.0 | -1.0 | -r-nastiseq | -Up-to-date | -- | - | - | - | A method to identify cis-NATs using ssRNA-seq | -- | - | Up-to-date | -https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ | -RNA | -nastiseq | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq | -
- | paralyzer | -1.5 | -1.5 | -paralyzer | -Up-to-date | -- | - | - | - | A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. | -- | - | Up-to-date | -https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ | -RNA | -paralyzer | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer | -
- | pipmir | -0.1.0 | -1.1 | -pipmir | -To update | -- | - | - | - | A method to identify novel plant miRNA. | -- | - | To update | -https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ | -RNA | -pipmir | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir | -
- | rRNA | -0.1 | -- | hmmsearch3.0 | -To update | -- | - | - | - | Identification of ribosomal RNA genes in metagenomic fragments. | -- | - | To update | -http://weizhong-lab.ucsd.edu/meta_rna/ | -RNA | -rrna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rRNA | -
- | rbpbench | -0.8.1 | -0.8.1 | -rbpbench | -Up-to-date | -rbpbench | -RBPBench | -- | RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis | -Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs | -Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs | -- | Up-to-date | -https://github.com/michauhl/RBPBench | -Sequence Analysis, RNA, CLIP-seq | -rbpbench | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench | -
- | rcas | -1.5.4 | -1.28.2 | -bioconductor-rcas | -To update | -- | - | - | - | RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments | -- | - | To update | -https://github.com/BIMSBbioinfo/RCAS | -RNA | -rcas | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ | -
- | reago | -1.1 | -1.1 | -reago | -Up-to-date | -- | - | - | - | Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. | -- | - | Up-to-date | -https://github.com/chengyuan/reago-1.1 | -Metagenomics, RNA | -reago | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago | -
- | remurna | -1.0.0 | -1.0 | -remurna | -To update | -- | - | - | - | remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation | -- | - | To update | -https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna | -RNA | -remurna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna | -
- | ribotaper | -1.3.1a | -1.3.1 | -ribotaper | -To update | -ribotaper | -RiboTaper | -Gene expression profiling | -Functional genomics | -A method for defining traslated ORFs using Ribosome Profiling data. | -New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. | -- | To update | -https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ | -RNA | -ribotaper | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ | -
- | rna_shapes | -3.3.0 | -- | @EXECUTABLE@ | -To update | -- | - | - | - | Compute secondary structures of RNA | -- | - | To update | -- | RNA | -rnashapes | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes | -
- | rnabob | -2.2.1.0 | -2.2.1 | -rnabob | -To update | -- | - | - | - | Fast pattern searching for RNA structural motifs | -- | - | To update | -http://eddylab.org/software.html | -RNA | -rnabob | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob | -
- | rnacode | -0.3.2 | -0.3 | -rnacode | -To update | -- | - | - | - | Analyze the protein coding potential in MSA | -- | - | To update | -- | RNA | -rnacode | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode | -
- | rnacommender | -0.1.1 | -3.5 | -sam | -To update | -- | - | - | - | RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. | -- | - | To update | -https://github.com/gianlucacorrado/RNAcommender | -RNA | -rnacommender | -rnateam | -https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender | -
- | rnalien | -1.3.6 | -1.8.0 | -rnalien | -To update | -- | - | - | - | RNAlien unsupervized RNA family model construction | -- | - | To update | -http://rna.tbi.univie.ac.at/rnalien/ | -RNA, Sequence Analysis | -rnalien | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien | -
- | rnasnp | -1.2.0 | -1.2 | -rnasnp | -To update | -- | - | - | - | RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs | -- | - | To update | -http://rth.dk/resources/rnasnp/ | -RNA | -rnasnp | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp | -
- | rnaz | -2.1.1 | -2.1.1 | -rnaz | -Up-to-date | -- | - | - | - | RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. | -- | - | Up-to-date | -https://www.tbi.univie.ac.at/~wash/RNAz/ | -RNA | -rnaz | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz | -
- | selectsequencesfrommsa | -1.0.5 | -1.0.5 | -selectsequencesfrommsa | -Up-to-date | -- | - | - | - | SelectSequences - selects representative entries from a multiple sequence alignment in clustal format | -- | - | Up-to-date | -https://github.com/eggzilla/SelectSequences | -RNA, Sequence Analysis | -selectsequencesfrommsa | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa | -
- | sortmerna | -4.3.6 | -4.3.6 | -sortmerna | -Up-to-date | -sortmerna | -SortMeRNA | -Sequence similarity search, Sequence comparison, Sequence alignment analysis | -Metatranscriptomics, Metagenomics | -SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. | -Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. | -- | Up-to-date | -http://bioinfo.lifl.fr/RNA/sortmerna/ | -RNA | -sortmerna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna | -
- | sshmm | -1.0.7 | -1.0.7 | -sshmm | -Up-to-date | -- | - | - | - | ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data | -- | - | Up-to-date | -https://github.molgen.mpg.de/heller/ssHMM | -Sequence Analysis, RNA | -sshmm | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ | -
- | targetfinder | -1.7 | -1.7 | -targetfinder | -Up-to-date | -- | - | - | - | Plant small RNA target prediction tool | -- | - | Up-to-date | -https://github.com/carringtonlab/TargetFinder.git | -RNA | -targetfinder | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ | -
- | trna_prediction | -0.6 | -1.2.41 | -aragorn | -To update | -- | - | - | - | Aragorn predicts tRNA and tmRNA in nucleotide sequences. | -- | - | To update | -http://mbioserv2.mbioekol.lu.se/ARAGORN/ | -RNA | -trna_prediction | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction | -
- | vienna_rna | -2.2.10 | -2.6.4 | -viennarna | -To update | -- | - | - | - | ViennaRNA - Prediction and comparison of RNA secondary structures | -- | - | To update | -http://www.tbi.univie.ac.at/RNA/ | -RNA | -viennarna | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna | -
- | sailfish | -0.10.1.1 | -- | bzip2 | -To update | -- | - | - | - | Sailfish is a tool for transcript quantification from RNA-seq data | -- | - | To update | -http://www.cs.cmu.edu/~ckingsf/software/sailfish/ | -Sequence Analysis, RNA | -sailfish | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/sailfish | -
- | salmon | -1.10.1 | -1.10.2 | -salmon | -To update | -- | - | - | - | Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. | -- | - | To update | -https://github.com/COMBINE-lab/salmon | -Sequence Analysis, RNA, Transcriptomics | -- | bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/salmon | -
- | sambamba | -- | 1.0 | -sambamba | -To update | -- | - | - | - | SAMBAMBA: process your BAM data faster! | -- | - | To update | -https://github.com/lomereiter/sambamba | -SAM | -sambamba | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/sambamba | -
- | sed | -0.0.1 | -- | sed | -To update | -- | - | - | - | Manipulate your data with the sed command line tool. | -- | - | To update | -https://github.com/bgruening/galaxytools/tree/master/tools/sed | -Text Manipulation | -sed_wrapper | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/sed | -
- | segemehl | -0.2.0.4 | -0.3.4 | -segemehl | -To update | -- | - | - | - | segemehl - short read mapping with gaps | -- | - | To update | -http://www.bioinf.uni-leipzig.de/Software/segemehl/ | -Next Gen Mappers | -segemehl | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/segemehl | -
- | sklearn | -1.0.11.0 | -- | - | To update | -- | - | - | - | Machine Learning tool suite from Scikit-learn | -- | - | To update | -http://scikit-learn.org | -Machine Learning, Statistics | -sklearn | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/sklearn | -
- | splitfasta | -0.4.0 | -1.70 | -biopython | -To update | -- | - | - | - | Split a multi-sequence fasta file into files containing single sequences | -- | - | To update | -- | Text Manipulation | -splitfasta | -rnateam | -https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta | -
- | statistics | -0.3 | -- | numpy | -To update | -- | - | - | - | Tool for computing statistical tests. | -- | - | To update | -https://github.com/bgruening/galaxytools/tree/master/tools/statistics | -Statistics | -bg_statistical_hypothesis_testing | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/statistics | -
- | stress_ng | -0.12.04 | -- | stress-ng | -To update | -- | - | - | - | stress test a computer system in various selectable ways | -- | - | To update | -- | Web Services | -stress_ng | -bgruening-util | -https://github.com/ColinIanKing/stress-ng | -
- | tapscan | -4.76+galaxy0 | -3.4 | -hmmer | -To update | -- | - | - | - | Search for transcription associated proteins (TAPs) | -- | - | To update | -https://plantcode.cup.uni-freiburg.de/tapscan/ | -Proteomics | -tapscan | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/tapscan | -
- | add_line_to_file | -0.1.0 | -8.25 | -coreutils | -To update | -- | - | - | - | Adds a text line to the beginning or end of a file. | -- | - | To update | -- | Text Manipulation | -add_line_to_file | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file | -
- | column_arrange_by_header | -0.2 | -- | - | To update | -- | - | - | - | Column arrange by header name | -- | - | To update | -- | Text Manipulation | -column_arrange_by_header | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header | -
- | join_files_on_column_fuzzy | -1.0.1 | -- | python | -To update | -- | - | - | - | Join two files on a common column, allowing a certain difference. | -- | - | To update | -- | Text Manipulation | -join_files_on_column_fuzzy | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy | -
- | split_file_on_column | -0.6 | -- | gawk | -To update | -- | - | - | - | Split a file on a specific column. | -- | - | To update | -- | Text Manipulation | -split_file_on_column | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column | -
- | split_file_to_collection | -0.5.1 | -- | python | -To update | -- | - | - | - | Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. | -- | - | To update | -- | Text Manipulation | -split_file_to_collection | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection | -
- | text_processing | -9.3 | -8.25 | -coreutils | -To update | -- | - | - | - | High performance text processing tools using the GNU coreutils, sed, awk and friends. | -- | - | To update | -https://www.gnu.org/software/ | -Text Manipulation | -text_processing | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing | -
- | tgsgapcloser | -1.0.3 | -1.2.1 | -tgsgapcloser | -To update | -TGS-GapCloser | -TGS-GapCloser | -Genome assembly, Read mapping, Scaffolding, Localised reassembly | -Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping | -TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. | -TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. | -- | To update | -https://github.com/BGI-Qingdao/TGS-GapCloser | -Assembly | -tgsgapcloser | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser | -
- | tool_recommendation_model | -0.0.5 | -- | python | -To update | -- | - | - | - | Create model to recommend tools | -- | - | To update | -https://github.com/bgruening/galaxytools | -Machine Learning | -create_tool_recommendation_model | -bgruening | -https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model | -
- | trim_galore | -0.6.7 | -0.6.10 | -trim-galore | -To update | -trim_galore | -Trim Galore | -Sequence trimming | -Sequence analysis | -Trim Galore adaptive quality and adapter trimmer | -A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. | -- | To update | -http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ | -Sequence Analysis, Fastq Manipulation | -trim_galore | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore | -
- | uniprot_rest_interface | -0.4 | -- | requests | -To update | -- | - | - | - | UniProt ID mapping and sequence retrieval | -- | - | To update | -https://github.com/jdrudolph/uniprot | -Proteomics, Sequence Analysis | -uniprot_rest_interface | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface | -
- | vt | -0.2 | -2015.11.10 | -vt | -To update | -- | - | - | - | A tool set for short variant discovery in genetic sequence data. | -- | - | To update | -- | Sequence Analysis, Variant Analysis | -vt | -bgruening | -https://github.com/atks/vt | -
- | wtdbg | -2.5 | -2.5 | -wtdbg | -Up-to-date | -wtdbg2 | -wtdbg2 | -Genome assembly, De-novo assembly | -Sequence assembly, Sequencing | -WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. | -Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. | -- | Up-to-date | -https://github.com/ruanjue/wtdbg2 | -Assembly | -wtdbg | -bgruening | -https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg | -
- | align_back_trans | -0.0.10 | -1.70 | -biopython | -To update | -- | - | - | - | Thread nucleotides onto a protein alignment (back-translation) | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans | -Fasta Manipulation, Sequence Analysis | -align_back_trans | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans | -
- | chromosome_diagram | -0.0.3 | -1.70 | -biopython | -To update | -- | - | - | - | Chromosome Diagrams using Biopython | -- | - | To update | -- | Graphics, Sequence Analysis, Visualization | -chromosome_diagram | -peterjc | -- |
- | clc_assembly_cell | -0.0.7 | -1.19.2 | -samtools | -To update | -- | - | - | - | Galaxy wrapper for the CLC Assembly Cell suite from CLCBio | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell | -Assembly, Next Gen Mappers, SAM | -clc_assembly_cell | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell | -
- | clinod | -0.1.0 | -1.3 | -clinod | -To update | -- | - | - | - | NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins | -- | - | To update | -http://www.compbio.dundee.ac.uk/www-nod/ | -Sequence Analysis | -clinod | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod | -
- | count_roi_variants | -0.0.6 | -1.19.2 | -samtools | -To update | -- | - | - | - | Count sequence variants in region of interest in BAM file | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants | -Assembly, SAM | -count_roi_variants | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants | -
- | coverage_stats | -0.1.0 | -1.19.2 | -samtools | -To update | -- | - | - | - | BAM coverage statistics using samtools idxstats and depth | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats | -Assembly, SAM | -coverage_stats | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats | -
- | effectiveT3 | -0.0.20 | -1.0.1 | -effectiveT3 | -To update | -- | - | - | - | Find bacterial type III effectors in protein sequences | -- | - | To update | -http://effectors.org | -Sequence Analysis | -effectivet3 | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 | -
- | fasta_filter_by_id | -0.0.7 | -1.1.5 | -galaxy_sequence_utils | -To update | -- | - | - | - | Filter FASTA sequences by ID (DEPRECATED) | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id | -Fasta Manipulation, Sequence Analysis, Text Manipulation | -fasta_filter_by_id | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id | -
- | fastq_filter_by_id | -0.0.7 | -1.1.5 | -galaxy_sequence_utils | -To update | -- | - | - | - | Filter FASTQ sequences by ID (DEPRECATED) | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id | -Fastq Manipulation, Sequence Analysis, Text Manipulation | -fastq_filter_by_id | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id | -
- | fastq_pair_names | -0.0.5 | -1.1.5 | -galaxy_sequence_utils | -To update | -- | - | - | - | Extract FASTQ paired read names | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names | -Sequence Analysis | -fastq_pair_names | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names | -
- | fastq_paired_unpaired | -0.1.5 | -1.1.5 | -galaxy_sequence_utils | -To update | -- | - | - | - | Divide FASTQ file into paired and unpaired reads | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired | -Sequence Analysis, Text Manipulation | -fastq_paired_unpaired | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired | -
- | get_orfs_or_cdss | -0.2.3 | -1.70 | -biopython | -To update | -- | - | - | - | Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss | -Sequence Analysis | -get_orfs_or_cdss | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss | -
- | mummer | -0.0.8 | -9.18 | -ghostscript | -To update | -- | - | - | - | Draw dotplots using mummer, mucmer, or promer with mummerplot | -- | - | To update | -http://mummer.sourceforge.net/ | -Graphics, Sequence Analysis, Visualization | -mummer | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer | -
- | nlstradamus | -0.0.11 | -1.8 | -NLStradamus | -To update | -- | - | - | - | Find nuclear localization signals (NLSs) in protein sequences | -- | - | To update | -http://www.moseslab.csb.utoronto.ca/NLStradamus | -Fasta Manipulation, Sequence Analysis | -nlstradamus | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus | -
- | predictnls | -0.0.10 | -- | - | To update | -- | - | - | - | Python reimplementation of predictNLS for Galaxy | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls | -Sequence Analysis | -predictnls | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls | -
- | protein_analysis | -0.0.13 | -- | promoter | -To update | -- | - | - | - | TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis | -Sequence Analysis | -tmhmm_and_signalp | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis | -
- | sample_seqs | -0.2.6 | -1.70 | -biopython | -To update | -- | - | - | - | Sub-sample sequences files (e.g. to reduce coverage) | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs | -Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis | -sample_seqs | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs | -
- | samtools_depad | -0.0.5 | -1.19.2 | -samtools | -To update | -- | - | - | - | Re-align a SAM/BAM file with a padded reference (using samtools depad) | -- | - | To update | -http://www.htslib.org/ | -Assembly, SAM, Sequence Analysis | -samtools_depad | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad | -
- | samtools_depth | -0.0.3 | -1.19.2 | -samtools | -To update | -- | - | - | - | Coverage depth via samtools | -- | - | To update | -http://www.htslib.org/ | -Assembly, Sequence Analysis, SAM | -samtools_depth | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth | -
- | samtools_idxstats | -0.0.6 | -1.19.2 | -samtools | -To update | -- | - | - | - | BAM mapping statistics (using samtools idxstats) | -- | - | To update | -http://www.htslib.org/ | -Assembly, Next Gen Mappers, SAM | -samtools_idxstats | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats | -
- | seq_composition | -0.0.5 | -1.70 | -biopython | -To update | -- | - | - | - | Sequence composition | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition | -Sequence Analysis | -seq_composition | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition | -
- | seq_filter_by_id | -0.2.9 | -1.70 | -biopython | -To update | -- | - | - | - | Filter sequences by ID | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id | -Fasta Manipulation, Sequence Analysis, Text Manipulation | -seq_filter_by_id | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id | -
- | seq_filter_by_mapping | -0.0.8 | -1.70 | -biopython | -To update | -- | - | - | - | Filter sequencing reads using SAM/BAM mapping files | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping | -Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis | -seq_filter_by_mapping | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping | -
- | seq_length | -0.0.5 | -1.70 | -biopython | -To update | -- | - | - | - | Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length | -Fasta Manipulation, Fastq Manipulation, Sequence Analysis | -seq_length | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length | -
- | seq_primer_clip | -0.0.18 | -1.1.5 | -galaxy_sequence_utils | -To update | -- | - | - | - | Trim off 5' or 3' primers | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip | -Assembly, Fasta Manipulation, Text Manipulation | -seq_primer_clip | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip | -
- | seq_rename | -0.0.10 | -1.1.5 | -galaxy_sequence_utils | -To update | -- | - | - | - | Rename sequences with ID mapping from a tabular file | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename | -Fasta Manipulation, Sequence Analysis, Text Manipulation | -seq_rename | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename | -
- | seq_select_by_id | -0.0.15 | -1.70 | -biopython | -To update | -- | - | - | - | Select sequences by ID | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id | -Fasta Manipulation, Sequence Analysis, Text Manipulation | -seq_select_by_id | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id | -
- | venn_list | -0.1.2 | -1.1.5 | -galaxy_sequence_utils | -To update | -- | - | - | - | Draw Venn Diagram (PDF) from lists, FASTA files, etc | -- | - | To update | -https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list | -Graphics, Sequence Analysis, Visualization | -venn_list | -peterjc | -https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list | -
- | TrimNs | -0.1.0 | -1.0 | -trimns_vgp | -To update | -- | - | - | - | TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline | -- | - | To update | -https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs | -Assembly | -trimns | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN | -
- | abricate | -1.0.1 | -1.0.1 | -abricate | -Up-to-date | -ABRicate | -ABRicate | -Antimicrobial resistance prediction | -Genomics, Microbiology | -Mass screening of contigs for antiobiotic resistance genes | -Mass screening of contigs for antimicrobial resistance or virulence genes. | -- | Up-to-date | -https://github.com/tseemann/abricate | -Sequence Analysis | -abricate | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ | -
- | abritamr | -1.0.14 | -1.0.14 | -abritamr | -Up-to-date | -- | - | - | - | A pipeline for running AMRfinderPlus and collating results into functional classes | -- | - | Up-to-date | -https://zenodo.org/record/7370628 | -Sequence Analysis | -abritamr | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr | -
- | abyss | -2.3.7 | -2.3.7 | -abyss | -Up-to-date | -abyss | -ABySS | -Genome assembly, De-novo assembly, Scaffolding | -Sequence assembly | -Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler | -De novo genome sequence assembler using short reads. | -- | Up-to-date | -http://www.bcgsc.ca/platform/bioinfo/software/abyss | -Assembly | -abyss | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss | -
- | adapter_removal | -2.3.3 | -2.3.3 | -adapterremoval | -Up-to-date | -adapterremoval | -AdapterRemoval | -Sequence trimming, Sequence merging, Primer removal | -- | Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. | -AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. | -- | Up-to-date | -https://github.com/MikkelSchubert/adapterremoval | -Fasta Manipulation, Sequence Analysis | -adapter_removal | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ | -
- | add_input_name_as_column | -0.2.0 | -- | python | -To update | -- | - | - | - | Add input name as column on an existing tabular file | -- | - | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column | -Text Manipulation | -add_input_name_as_column | -mvdbeek | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column | -
- | aegean | -0.16.0 | -0.16.0 | -aegean | -Up-to-date | -gaeval | -GAEVAL | -Sequence annotation | -Sequence analysis, Gene structure | -AEGeAn toolkit wrappers | -Gene Annotation EVAluation. | -- | Up-to-date | -https://github.com/BrendelGroup/AEGeAn | -Transcriptomics, Sequence Analysis | -aegean | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean | -
- | aldex2 | -1.26.0 | -1.34.0 | -bioconductor-aldex2 | -To update | -aldex2 | -ALDEx2 | -Statistical inference | -Gene expression, Statistics and probability | -Performs analysis Of differential abundance taking sample variation into account | -A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. | -- | To update | -https://github.com/ggloor/ALDEx_bioc | -Metagenomics | -aldex2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 | -
- | allegro | -@VER@.0 | -3 | -allegro | -To update | -allegro | -Allegro | -Sequence motif discovery | -Sequence analysis, Transcription factors and regulatory sites, DNA | -Linkage and haplotype analysis from deCODE | -It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. | -- | To update | -http://www.decode.com/software/ | -Variant Analysis | -allegro | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ | -
- | amplican | -1.14.0 | -1.24.0 | -bioconductor-amplican | -To update | -amplican | -amplican | -Alignment, Standardisation and normalisation | -PCR experiment, Statistics and probability | -AmpliCan is an analysis tool for genome editing. | -It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. | -- | To update | -https://github.com/valenlab/amplican | -Sequence Analysis | -amplican | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican | -
- | ampvis2 | -2.8.6 | -- | - | To update | -ampvis | -ampvis | -Analysis, Visualisation | -Biodiversity | -ampvis2 | -ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. | -- | To update | -https://github.com/MadsAlbertsen/ampvis2/ | -Metagenomics | -ampvis2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 | -
- | amrfinderplus | -3.11.26 | -3.12.8 | -ncbi-amrfinderplus | -To update | -amrfinderplus | -AMRFinderPlus | -Antimicrobial resistance prediction | -Microbiology, Public health and epidemiology, Infectious disease | -"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. | -AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms | -- | To update | -https://github.com/ncbi/amr | -Sequence Analysis | -AMRFinderPlus | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus | -
- | ancombc | -1.4.0 | -2.4.0 | -bioconductor-ancombc | -To update | -ancombc | -ANCOMBC | -DNA barcoding | -Microbial ecology, Metagenomics | -Performs analysis of compositions of microbiomes with bias correction. | -Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. | -- | To update | -https://github.com/FrederickHuangLin/ANCOMBC | -Metagenomics | -ancombc | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc | -
- | anndata | -0.10.3 | -0.6.22.post1 | -anndata | -To update | -- | - | - | - | Import, Export, Inspect and Manipulate Anndata and Loom objects | -- | - | To update | -https://anndata.readthedocs.io | -Transcriptomics, Sequence Analysis | -anndata | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ | -
- | annotatemyids | -3.18.0 | -3.18.0 | -bioconductor-org.hs.eg.db | -Up-to-date | -annotatemyids | -annotatemyids | -Annotation | -- | annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages | -This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. | -- | Up-to-date | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids | -Genome annotation | -annotatemyids | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids | -
- | arriba | -2.4.0 | -2.4.0 | -arriba | -Up-to-date | -- | - | - | - | Arriba detects fusion genes in RNA-Seq data after running RNA-STAR | -- | - | Up-to-date | -https://github.com/suhrig/arriba | -Sequence Analysis, Transcriptomics | -arriba | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba | -
- | art | -2014.11.03.0 | -2016.06.05 | -art | -To update | -art | -ART | -Conversion | -Bioinformatics | -Simulator for Illumina, 454, and SOLiD sequencing data | -ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD | -- | To update | -- | Sequence Analysis, Data Source | -art | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/art | -
- | artic | -- | 1.2.4 | -artic | -To update | -artic | -ARTIC | -Sequence alignment | -Genomics | -The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building | -A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore | -- | To update | -https://github.com/artic-network/fieldbioinformatics | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic | -
- | assembly-stats | -17.02 | -17.02 | -rjchallis-assembly-stats | -Up-to-date | -- | - | - | - | Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. | -- | - | Up-to-date | -https://github.com/rjchallis/assembly-stats | -Assembly | -assembly_stats | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats | -
- | augustus | -3.4.0 | -3.5.0 | -augustus | -To update | -augustus | -AUGUSTUS | -Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation | -Gene transcripts, Gene and protein families | -AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. | -AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. | -- | To update | -http://bioinf.uni-greifswald.de/augustus/ | -Sequence Analysis | -augustus | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus | -
- | b2btools | -3.0.5+galaxy0 | -3.0.6 | -b2btools | -To update | -b2btools | -b2bTools | -Protein disorder prediction, Protein secondary structure prediction, Protein feature detection | -- | This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. | -The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA | -- | To update | -https://bio2byte.be | -Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology | -- | iuc | -- |
- | bakta | -1.9.2 | -1.9.2 | -bakta | -Up-to-date | -Bakta | -Bakta | -Genome annotation | -Genomics, Data submission, annotation and curation, Sequence analysis | -"Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." | -Rapid & standardized annotation of bacterial genomes, MAGs & plasmids | -- | Up-to-date | -https://github.com/oschwengers/bakta | -Sequence Analysis | -bakta | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta | -
- | bam_to_scidx | -1.0.1 | -- | openjdk | -To update | -- | - | - | - | Contains a tool that converts a BAM file to an ScIdx file. | -- | - | To update | -https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx | -Convert Formats | -bam_to_scidx | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx | -
- | bamutil | -- | 1.0.15 | -bamutil | -To update | -- | - | - | - | bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. | -- | - | To update | -https://github.com/statgen/bamUtil | -Sequence Analysis | -bamutil | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil | -
- | bandage | -2022.09 | -2022.09 | -bandage_ng | -Up-to-date | -bandage | -Bandage | -Sequence assembly visualisation | -Genomics, Sequence assembly | -Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily | -GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. | -- | Up-to-date | -https://github.com/rrwick/Bandage | -Visualization | -bandage | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage | -
- | barcode_splitter | -0.18.4.0 | -0.18.6 | -barcode_splitter | -To update | -- | - | - | - | A utility to split sequence files using multiple sets of barcodes | -- | - | To update | -https://bitbucket.org/princeton_genomics/barcode_splitter/ | -Fastq Manipulation | -barcode_splitter | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter | -
- | baredsc | -1.1.2 | -1.1.2 | -baredsc | -Up-to-date | -baredsc | -baredSC | -Data retrieval, Expression correlation analysis, Differential gene expression profiling | -RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability | -baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. | -The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. | -- | Up-to-date | -https://github.com/lldelisle/baredSC | -Transcriptomics, Visualization | -baredsc | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc | -
- | barrnap | -1.2.2 | -0.9 | -barrnap | -To update | -barrnap | -Barrnap | -Gene prediction | -Genomics, Model organisms, Model organisms | -Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. | -Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). | -- | To update | -- | Sequence Analysis | -barrnap | -iuc | -- |
- | basil | -1.2.0 | -1.2.0 | -anise_basil | -Up-to-date | -- | - | - | - | Breakpoint detection, including large insertions | -- | - | Up-to-date | -https://github.com/seqan/anise_basil | -Variant Analysis | -basil | -iuc | -- |
- | bax2bam | -0.0.11 | -0.0.11 | -bax2bam | -Up-to-date | -- | - | - | - | BAX to BAM converter | -- | - | Up-to-date | -https://github.com/pacificbiosciences/bax2bam/ | -Convert Formats, Sequence Analysis | -bax2bam | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam | -
- | bayescan | -2.1 | -2.0.1 | -bayescan | -To update | -bayescan | -BayeScan | -Statistical inference | -Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism | -Detecting natural selection from population-based genetic data | -BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. | -- | To update | -http://cmpg.unibe.ch/software/BayeScan/index.html | -Sequence Analysis | -bayescan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ | -
- | bbtools | -39.06 | -39.06 | -bbmap | -Up-to-date | -- | - | - | - | BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. | -- | - | Up-to-date | -https://jgi.doe.gov/data-and-tools/bbtools/ | -Sequence Analysis | -bbtools | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools | -
- | bcftools | -1.15.1 | -1.19 | -bcftools | -To update | -bcftools | -BCFtools | -Data handling, Variant calling | -Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment | -BCFtools toolkit wrappers | -BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. | -- | To update | -https://samtools.github.io/bcftools/ | -Variant Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools | -
- | bctools | -0.2.2 | -0.2.2 | -bctools | -Up-to-date | -- | - | - | - | bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 | -- | - | Up-to-date | -https://github.com/dmaticzka/bctools | -Sequence Analysis, Transcriptomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools | -
- | beacon2 | -2.0.0 | -2.0.0 | -beacon2-ri-tools | -Up-to-date | -GA4GH Beacon | -- | - | - | beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). | -- | - | Up-to-date | -https://github.com/EGA-archive/beacon2-ri-tools/tree/main | -Variant Analysis | -beacon2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 | -
- | beagle | -5.2_21Apr21.304 | -5.4_22Jul22.46e | -beagle | -To update | -- | - | - | - | Beagle is a program for phasing and imputing missing genotypes. | -- | - | To update | -https://faculty.washington.edu/browning/beagle/beagle.html | -Variant Analysis | -beagle | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle | -
- | bedops | -2.4.41 | -2.4.41 | -bedops | -Up-to-date | -- | - | - | - | BEDOPS: high-performance genomic feature operations | -- | - | Up-to-date | -https://bedops.readthedocs.io/en/latest/ | -Genomic Interval Operations | -bedops_sortbed | -iuc | -https://bedops.readthedocs.io/ | -
- | bedtools | -2.30.0 | -2.31.1 | -bedtools | -To update | -bedtools | -BEDTools | -Mapping | -Genomics | -bedtools is a powerful toolset for genome arithmetic | -BEDTools is an extensive suite of utilities for comparing genomic features in BED format. | -- | To update | -https://github.com/arq5x/bedtools2 | -Genomic Interval Operations, Text Manipulation | -bedtools | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools | -
- | bellerophon | -1.0 | -1.0 | -bellerophon | -Up-to-date | -- | - | - | - | Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. | -- | - | Up-to-date | -https://github.com/davebx/bellerophon | -Sequence Analysis | -bellerophon | -iuc | -https://github.com/davebx/bellerophon | -
- | berokka | -0.2.3 | -0.2.3 | -berokka | -Up-to-date | -- | - | - | - | Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. | -- | - | Up-to-date | -https://github.com/tseemann/berokka | -Fasta Manipulation | -berokka | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka | -
- | bigscape | -1.1.9 | -1.1.9 | -bigscape | -Up-to-date | -- | - | - | - | Construct sequence similarity networks of BGCs and groups them into GCF | -- | - | Up-to-date | -https://github.com/medema-group/BiG-SCAPE | -Metagenomics | -bigscape | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ | -
- | binning_refiner | -1.4.3 | -1.4.3 | -binning_refiner | -Up-to-date | -binning_refiner | -Binning_refiner | -Read binning, Sequence clustering | -Metagenomics | -Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. | -Improving genome bins through the combination of different binning programs | -- | Up-to-date | -https://github.com/songweizhi/Binning_refiner | -Metagenomics | -binning_refiner | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ | -
- | bioext | -0.21.2 | -0.21.2 | -python-bioext | -Up-to-date | -- | - | - | - | A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! | -- | - | Up-to-date | -https://pypi.python.org/pypi/biopython-extensions/ | -Next Gen Mappers | -- | iuc | -https://github.com/davebx/bioext-gx/ | -
- | bioinformatics_cafe | -0.1.0 | -- | python | -To update | -- | - | - | - | Miscellanea of scripts for bioinformatics | -- | - | To update | -https://github.com/dariober/bioinformatics-cafe/ | -Sequence Analysis | -bioinformatics_cafe | -mbernt | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe | -
- | biom_format | -2.1.15 | -2.1.7 | -biom-format | -To update | -biomformat | -biomformat | -Formatting | -Laboratory information management, Sequence analysis | -The biom-format package provides a command line interface and Python API for working with BIOM files. | -This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. | -- | To update | -https://github.com/biocore/biom-format | -Metagenomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format | -
- | bioperl | -1.1 | -1.7.8 | -perl-bioperl | -To update | -bioperl | -BioPerl | -Data handling, Service invocation | -Genomics, Software engineering, Data management | -Converts GenBank format files to GFF3 | -A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. | -- | To update | -https://bioperl.org/ | -Sequence Analysis | -bp_genbank2gff3 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl | -
- | biscot | -2.3.3 | -2.3.3 | -biscot | -Up-to-date | -- | - | - | - | Bionano scaffolding correction tool | -- | - | Up-to-date | -https://github.com/institut-de-genomique/biscot | -Assembly | -biscot | -iuc | -https://github.com/bgruening/iuc/tree/master/tools/biscot | -
- | blast | -1.7.0 | -1.7.0 | -magicblast | -Up-to-date | -- | - | - | - | Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome | -- | - | Up-to-date | -https://ncbi.github.io/magicblast/ | -Next Gen Mappers | -magicblast | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast | -
- | blastxml_to_gapped_gff3 | -1.1 | -0.6.6 | -bcbiogff | -To update | -- | - | - | - | BlastXML to gapped GFF3 | -- | - | To update | -- | Convert Formats, Sequence Analysis | -blastxml_to_gapped_gff3 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 | -
- | bowtie2 | -2.5.3 | -2.5.3 | -bowtie2 | -Up-to-date | -bowtie2 | -Bowtie 2 | -Read mapping | -Mapping, Genomics, Mapping | -Bowtie2: Fast and sensitive read alignment | -Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. | -- | Up-to-date | -http://bowtie-bio.sourceforge.net/bowtie2 | -Next Gen Mappers | -bowtie2 | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 | -
- | bracken | -2.9 | -2.9 | -bracken | -Up-to-date | -bracken | -Bracken | -Statistical calculation | -Metagenomics, Microbial ecology | -Bayesian Reestimation of Abundance with KrakEN | -Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. | -- | Up-to-date | -https://ccb.jhu.edu/software/bracken/ | -Sequence Analysis, Metagenomics | -bracken | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken | -
- | breseq | -0.35.5 | -0.38.3 | -breseq | -To update | -breseq | -breseq | -Polymorphism detection | -Sequencing, Sequence analysis, DNA mutation | -Predicts mutations in microbial genomes | -Runs Breseq software on a set of fastq files. | -- | To update | -https://github.com/barricklab/breseq | -Variant Analysis | -breseq | -iuc | -- |
- | busco | -5.5.0 | -5.6.1 | -busco | -To update | -busco | -BUSCO | -Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly | -Sequence assembly, Genomics, Transcriptomics, Sequence analysis | -BUSCO assess genome and annotation completeness | -Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. | -- | To update | -https://gitlab.com/ezlab/busco/-/releases | -Sequence Analysis | -busco | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ | -
- | bwa | -0.7.17 | -0.7.17 | -bwa | -Up-to-date | -bwa | -BWA | -Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment | -Mapping | -Wrapper for bwa mem, aln, sampe, and samse | -Fast, accurate, memory-efficient aligner for short and long sequencing reads | -- | Up-to-date | -http://bio-bwa.sourceforge.net/ | -Next Gen Mappers | -bwa | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa | -
- | bwa_mem2 | -2.2.1 | -2.2.1 | -bwa-mem2 | -Up-to-date | -bwa-mem2 | -Bwa-mem2 | -Sequence alignment | -Mapping | -Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. | -Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. | -- | Up-to-date | -https://github.com/bwa-mem2/bwa-mem2 | -Next Gen Mappers | -bwa_mem2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 | -
- | bwameth | -0.2.6 | -0.2.7 | -bwameth | -To update | -- | - | - | - | Fast and accurate alignment of BS-seq reads | -- | - | To update | -https://github.com/brentp/bwa-meth | -Sequence Analysis, Next Gen Mappers | -bwameth | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth | -
- | cactus | -2.7.1 | -- | - | To update | -cactus | -Cactus | -Multiple sequence alignment, Genome alignment | -Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics | -Cactus is a reference-free whole-genome multiple alignment program | -Cactus is a reference-free whole-genome multiple alignment program. | -- | To update | -https://github.com/ComparativeGenomicsToolkit/cactus | -Sequence Analysis | -cactus | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus | -
- | calculate_contrast_threshold | -1.0.0 | -- | numpy | -To update | -- | - | - | - | Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. | -- | - | To update | -https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold | -Visualization, Genomic Interval Operations, SAM | -calculate_contrast_threshold | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold | -
- | calculate_numeric_param | -0.1.0 | -- | - | To update | -- | - | - | - | Calculate a numeric parameter value using integer and float values. | -- | - | To update | -- | Text Manipulation | -calculate_numeric_param | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param | -
- | cat | -5.2.3 | -5.3 | -cat | -To update | -cat_bins | -CAT and BAT | -Taxonomic classification, Sequence assembly, Coding region prediction | -Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly | -Contig Annotation Tool (CAT) | -Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. | -- | To update | -https://github.com/dutilh/CAT | -Metagenomics | -contig_annotation_tool | -iuc | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat | -
- | cdhit | -4.8.1 | -4.8.1 | -cd-hit | -Up-to-date | -cd-hit | -cd-hit | -Sequence clustering | -Sequencing | -Cluster or compare biological sequence datasets | -Cluster a nucleotide dataset into representative sequences. | -- | Up-to-date | -http://weizhongli-lab.org/cd-hit/ | -Sequence Analysis, Fasta Manipulation | -cd_hit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit | -
- | cemitool | -1.18.1 | -1.26.0 | -bioconductor-cemitool | -To update | -cemitool | -CEMiTool | -Enrichment analysis, Pathway or network analysis | -Gene expression, Transcriptomics, Microarray experiment | -Gene co-expression network analysis tool | -It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. | -- | To update | -https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html | -Transcriptomics, RNA, Statistics | -cemitool | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool | -
- | charts | -1.0.1 | -- | r-getopt | -To update | -- | - | - | - | Enables advanced visualization options in Galaxy Charts | -- | - | To update | -- | Visualization | -charts | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ | -
- | checkm | -1.2.0 | -1.2.2 | -checkm-genome | -To update | -checkm | -CheckM | -Operation | -Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics | -Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes | -CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. | -- | To update | -https://github.com/Ecogenomics/CheckM | -Metagenomics | -checkm | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm | -
- | cherri | -0.7 | -0.8 | -cherri | -To update | -cherri | -cherri | -- | Molecular interactions, pathways and networks, Structure analysis, Machine learning | -Computational Help Evaluating RNA-RNA interactions | -CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. | -- | To update | -https://github.com/BackofenLab/Cherri | -Transcriptomics, RNA | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri | -
- | chira | -1.4.3 | -1.4.3 | -chira | -Up-to-date | -chira | -ChiRA | -- | RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA | -Chimeric Read Annotator for RNA-RNA interactome data | -ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. | -- | Up-to-date | -https://github.com/pavanvidem/chira | -RNA, Transcriptomics, Sequence Analysis | -chira | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira | -
- | chopin2 | -1.0.7 | -- | chopin2 | -To update | -- | - | - | - | Domain-Agnostic Supervised Learning with Hyperdimensional Computing | -- | - | To update | -https://github.com/cumbof/chopin2 | -Machine Learning | -chopin2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 | -
- | chromeister | -1.5.a | -1.5.a | -chromeister | -Up-to-date | -- | - | - | - | ultra-fast pairwise genome comparisons | -- | - | Up-to-date | -https://github.com/estebanpw/chromeister | -Sequence Analysis | -chromeister | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister | -
- | circexplorer2 | -2.3.8 | -2.3.8 | -circexplorer2 | -Up-to-date | -circexplorer2 | -CIRCexplorer2 | -- | RNA splicing, Gene transcripts, Literature and language | -Comprehensive and integrative circular RNA analysis toolset. | -Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. | -- | Up-to-date | -https://github.com/YangLab/CIRCexplorer2 | -RNA, Assembly | -circexplorer2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 | -
- | circos | -0.69.8 | -0.69.9 | -circos | -To update | -galactic_circos | -Galactic Circos | -Sequence visualisation | -- | Build Circos Plots in Galaxy | -Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. | -- | To update | -http://circos.ca/ | -Graphics | -circos | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos | -
- | cite_seq_count | -1.4.4 | -1.4.4 | -cite-seq-count | -Up-to-date | -CITE-seq-Count | -CITE-seq-Count | -RNA-Seq quantification | -Transcriptomics, Immunoproteins and antigens | -Count CMO/HTO | -Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. | -- | Up-to-date | -https://github.com/Hoohm/CITE-seq-Count | -Transcriptomics | -cite_seq_count | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count | -
- | clair3 | -0.1.12 | -1.0.5 | -clair3 | -To update | -clair3 | -Clair3 | -Variant calling | -Molecular genetics | -Symphonizing pileup and full-alignment for high-performance long-read variant calling | -Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. | -- | To update | -https://github.com/HKU-BAL/Clair3 | -Sequence Analysis, Variant Analysis | -clair3 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 | -
- | clustalw | -2.1 | -2.1 | -clustalw | -Up-to-date | -\n clustal2\n | -- | - | - | ClustalW multiple sequence alignment program for DNA or proteins | -- | - | Up-to-date | -http://www.clustal.org/clustal2/ | -Phylogenetics, Sequence Analysis | -clustalw | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw | -
- | cnv-phenopacket | -1.0.2 | -- | cnv-phenopacket | -To update | -- | - | - | - | cnv-phenopacket Converts TSV metadata file to JSON. | -- | - | To update | -https://pypi.org/project/cnv-phenopacket/ | -Variant Analysis | -cnv_phenopacket | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket | -
- | cnv-vcf2json | -1.0.4 | -- | cnv-vcf2json | -To update | -- | - | - | - | cnv-vcf2json Converts structural variants VCF file to JSON. | -- | - | To update | -https://pypi.org/project/cnv-phenopacket/ | -Variant Analysis | -cnv-vcf2json | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json | -
- | cnvkit | -0.9.10 | -0.9.10 | -cnvkit | -Up-to-date | -cnvkit | -CNVkit | -Variant calling | -DNA structural variation | -detecting copy number variants and alterations genome-wide from high-throughput sequencing | -CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. | -- | Up-to-date | -https://github.com/etal/cnvkit | -Variant Analysis | -cnvkit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit | -
- | codeml | -4.9 | -4.10.7 | -paml | -To update | -paml | -PAML | -Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis | -Phylogenetics, Sequence analysis | -Detects positive selection | -Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. | -- | To update | -http://abacus.gene.ucl.ac.uk/software/paml.html | -Phylogenetics | -codeml | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml | -
- | cojac | -0.9.1 | -0.9.1 | -cojac | -Up-to-date | -cojac | -COJAC | -- | Genetic variation | -co-occurrence of mutations on amplicons | -CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. | -- | Up-to-date | -https://github.com/cbg-ethz/cojac | -Metagenomics, Sequence Analysis | -cojac | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac | -
- | colibread | -24.7.14+galaxy0 | -24.7.14 | -commet | -To update | -- | - | - | - | Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome | -- | - | To update | -https://colibread.inria.fr/ | -Sequence Analysis, Variant Analysis | -colibread | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread | -
- | collection_column_join | -0.0.3 | -8.25 | -coreutils | -To update | -- | - | - | - | Column Join on Collections | -- | - | To update | -- | Text Manipulation | -collection_column_join | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join | -
- | collection_element_identifiers | -0.0.2 | -- | - | To update | -- | - | - | - | Extract element identifiers of a collection | -- | - | To update | -- | Text Manipulation | -collection_element_identifiers | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers | -
- | column_maker | -2.0 | -- | python | -To update | -- | - | - | - | Compute an expression on every row | -- | - | To update | -- | Text Manipulation | -column_maker | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker | -
- | column_order_header_sort | -0.0.1 | -- | python | -To update | -- | - | - | - | Sort Column Order by heading | -- | - | To update | -- | Text Manipulation | -column_order_header_sort | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort | -
- | column_remove_by_header | -1.0 | -- | python | -To update | -- | - | - | - | Remove columns by header | -- | - | To update | -- | Text Manipulation | -column_remove_by_header | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header | -
- | compleasm | -0.2.5 | -0.2.5 | -compleasm | -Up-to-date | -- | - | - | - | Compleasm: a faster and more accurate reimplementation of BUSCO | -- | - | Up-to-date | -https://github.com/huangnengCSU/compleasm | -Sequence Analysis | -compleasm | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ | -
- | compose_text_param | -0.1.1 | -- | - | To update | -- | - | - | - | Compose a text parameter value using text, integer and float values | -- | - | To update | -- | Text Manipulation | -compose_text_param | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param | -
- | compress_file | -0.1.0 | -- | gzip | -To update | -- | - | - | - | Compress files. | -- | - | To update | -- | Text Manipulation | -compress_file | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file | -
- | concoct | -1.1.0 | -1.1.0 | -concoct | -Up-to-date | -concoct | -CONCOCT | -Sequence clustering, Read binning | -Metagenomics | -CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. | -A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. | -- | Up-to-date | -https://github.com/BinPro/CONCOCT | -Metagenomics | -concoct | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct | -
- | coverage_report | -0.0.4 | -1.76 | -perl-number-format | -To update | -- | - | - | - | Generate Detailed Coverage Report from BAM file | -- | - | To update | -https://github.com/galaxyproject/tools-iuc | -Sequence Analysis | -coverage_report | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report | -
- | coverm | -0.7.0 | -0.7.0 | -coverm | -Up-to-date | -coverm | -CoverM | -Local alignment | -Bioinformatics | -CoverM genome and contig wrappers | -Read coverage calculator for metagenomics | -- | Up-to-date | -https://github.com/wwood/CoverM | -Sequence Analysis | -coverm | -iuc | -https://github.com/galaxyproject/tools-iuc/tools/coverm | -
- | crispr_studio | -1+galaxy0 | -1 | -crispr_studio | -To update | -- | - | - | - | CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. | -- | - | To update | -https://github.com/moineaulab/CRISPRStudio | -Sequence Analysis | -crispr_studio | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ | -
- | crosscontamination_barcode_filter | -0.3 | -2.2.1 | -r-ggplot2 | -To update | -- | - | - | - | Barcode contamination discovery tool | -- | - | To update | -- | Transcriptomics, Visualization | -crosscontamination_barcode_filter | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter | -
- | crossmap | -0.6.1 | -0.7.0 | -crossmap | -To update | -- | - | - | - | CrossMap converts genome coordinates or annotation files between genome assemblies | -- | - | To update | -http://crossmap.sourceforge.net/ | -Convert Formats, Genomic Interval Operations | -crossmap | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap | -
- | cutadapt | -4.6 | -4.6 | -cutadapt | -Up-to-date | -cutadapt | -Cutadapt | -Sequence trimming | -Genomics, Probes and primers, Sequencing | -Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). | -Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. | -- | Up-to-date | -https://cutadapt.readthedocs.org/en/stable/ | -Fasta Manipulation, Fastq Manipulation, Sequence Analysis | -cutadapt | -lparsons | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt | -
- | cutesv | -1.0.8 | -2.1.0 | -cutesv | -To update | -cuteSV | -cuteSV | -Split read mapping, Genotyping, Structural variation detection | -DNA structural variation, Sequencing, Computer science | -Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. | -Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis | -- | To update | -https://github.com/tjiangHIT/cuteSV | -Variant Analysis | -cutesv | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv | -
- | cwpair2 | -1.1.1 | -- | matplotlib | -To update | -- | - | - | - | Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. | -- | - | To update | -- | ChIP-seq | -cwpair2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 | -
- | dada2 | -- | 1.30.0 | -bioconductor-dada2 | -To update | -dada2 | -dada2 | -Variant calling, DNA barcoding | -Sequencing, Genetic variation, Microbial ecology, Metagenomics | -DADA2 wrappers | -This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. | -- | To update | -https://benjjneb.github.io/dada2/index.html | -Metagenomics | -dada2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 | -
- | das_tool | -1.1.7 | -1.1.7 | -das_tool | -Up-to-date | -dastool | -dastool | -Read binning | -Metagenomics | -DAS Tool for genome resolved metagenomics | -DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. | -- | Up-to-date | -https://github.com/cmks/DAS_Tool | -Metagenomics | -das_tool | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool | -
- | data_source_iris_tcga | -1.0.0 | -- | python | -To update | -- | - | - | - | IRIS-TCGA Data source tool | -- | - | To update | -- | Data Source | -data_source_iris_tcga | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga | -
- | datamash | -1.8 | -1.1.0 | -datamash | -To update | -- | - | - | - | GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. | -- | - | To update | -https://www.gnu.org/software/datamash/ | -Text Manipulation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash | -
- | decontaminator | -1.0.0 | -- | numpy | -To update | -decontaminator | -- | - | - | Deep Learning method for novel virus detection in sequencing data | -- | - | To update | -https://github.com/cbib/decontaminator | -Machine Learning | -decontaminator | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator | -
- | deepmicro | -1.4 | -1.4 | -deepmicro | -Up-to-date | -\n DeepMicro\n | -- | - | - | Representation learning and classification framework | -- | - | Up-to-date | -https://github.com/paulzierep/DeepMicro | -Machine Learning | -deepmicro | -iuc | -https://github.com/paulzierep/DeepMicro | -
- | deepsig | -1.2.5 | -1.2.5 | -deepsig | -Up-to-date | -- | - | - | - | Predictor of signal peptides in proteins based on deep learning | -- | - | Up-to-date | -https://github.com/BolognaBiocomp/deepsig | -Genome annotation | -deepsig | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig | -
- | deepvariant | -1.5.0 | -- | - | To update | -- | - | - | - | DeepVariant is a deep learning-based variant caller | -- | - | To update | -https://github.com/google/deepvariant | -Variant Analysis | -deepvariant | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant | -
- | deg_annotate | -1.1.0 | -2.31.1 | -bedtools | -To update | -- | - | - | - | Annotate DESeq2/DEXSeq output tables | -- | - | To update | -- | Transcriptomics | -deg_annotate | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate | -
- | delly | -0.9.1 | -1.2.6 | -delly | -To update | -delly2 | -Delly2 | -Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis | -DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases | -Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. | -Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. | -- | To update | -https://github.com/dellytools/delly | -Variant Analysis | -delly | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly | -
- | deseq2 | -2.11.40.8 | -1.42.0 | -bioconductor-deseq2 | -To update | -DESeq2 | -DESeq2 | -Differential gene expression analysis | -Transcriptomics | -Differential gene expression analysis based on the negative binomial distribution | -R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. | -- | To update | -https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html | -Transcriptomics, RNA, Statistics | -deseq2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 | -
- | dexseq | -1.44 | -1.48.0 | -bioconductor-dexseq | -To update | -dexseq | -DEXSeq | -Enrichment analysis, Exonic splicing enhancer prediction | -RNA-Seq | -Inference of differential exon usage in RNA-Seq | -The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. | -- | To update | -https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html | -Transcriptomics, RNA, Statistics | -dexseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq | -
- | diamond | -2.0.15 | -2.1.9 | -diamond | -To update | -diamond | -Diamond | -Sequence alignment analysis | -Sequence analysis, Proteins | -DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. | -Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. | -- | To update | -https://github.com/bbuchfink/diamond | -Sequence Analysis | -diamond | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond | -
- | diffbind | -2.10.0 | -3.12.0 | -bioconductor-diffbind | -To update | -diffbind | -DiffBind | -Differential binding analysis | -ChIP-seq | -Diffbind provides functions for processing ChIP-Seq data. | -Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. | -- | To update | -http://bioconductor.org/packages/release/bioc/html/DiffBind.html | -ChIP-seq | -diffbind | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind | -
- | dimet | -0.2.1 | -0.2.2 | -dimet | -To update | -- | - | - | - | DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. | -- | - | To update | -https://github.com/cbib/DIMet | -Metabolomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet | -
- | disco | -- | 1.2 | -disco | -To update | -disco | -DISCO | -Protein sequence analysis | -Structure determination | -DISCO is a overlap-layout-consensus (OLC) metagenome assembler | -DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. | -- | To update | -http://disco.omicsbio.org/ | -Metagenomics, Assembly | -disco | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ | -
- | dnabot | -3.1.0 | -- | dnabot | -To update | -- | - | - | - | DNA assembly using BASIC on OpenTrons | -- | - | To update | -https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT | -Synthetic Biology | -dnabot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot | -
- | dnaweaver | -1.0.2 | -1.0.2 | -dnaweaver_synbiocad | -Up-to-date | -- | - | - | - | Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. | -- | - | Up-to-date | -https://github.com/Edinburgh-Genome-Foundry/DnaWeaver | -Synthetic Biology | -dnaweaver | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver | -
- | dram | -1.3.5 | -1.4.6 | -dram | -To update | -dram | -DRAM | -Gene functional annotation | -Metagenomics, Biological databases, Molecular genetics | -DRAM for distilling microbial metabolism to automate the curation of microbiome function | -Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes | -- | To update | -https://github.com/WrightonLabCSU/DRAM | -Metagenomics | -dram | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram | -
- | drep | -3.4.5 | -3.5.0 | -drep | -To update | -drep | -dRep | -Genome comparison | -Metagenomics, Genomics, Sequence analysis | -dRep compares and dereplicates genome sets | -Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. | -- | To update | -https://github.com/MrOlm/drep | -Metagenomics | -drep | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep | -
- | dropletutils | -1.10.0 | -1.22.0 | -bioconductor-dropletutils | -To update | -dropletutils | -DropletUtils | -Loading, Community profiling | -Gene expression, RNA-seq, Sequencing, Transcriptomics | -DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data | -Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. | -- | To update | -https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html | -Transcriptomics, Sequence Analysis | -dropletutils | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ | -
- | ebi_tools | -0.1.0 | -- | six | -To update | -- | - | - | - | Tools to query and download data from several EMBL-EBI databases | -- | - | To update | -http://www.ebi.ac.uk/services/all | -Web Services, Data Source | -ebi_tools | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools | -
- | edger | -3.36.0 | -4.0.2 | -bioconductor-edger | -To update | -edger | -edgeR | -Differential gene expression analysis | -Genetics, RNA-Seq, ChIP-seq | -Perform RNA-Seq differential expression analysis using edgeR pipeline | -Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. | -- | To update | -http://bioconductor.org/packages/release/bioc/html/edgeR.html | -Transcriptomics, RNA, Statistics | -edger | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger | -
- | egsea | -1.20.0 | -1.28.0 | -bioconductor-egsea | -To update | -egsea | -EGSEA | -Gene set testing | -Systems biology | -This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing | -This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. | -- | To update | -https://bioconductor.org/packages/release/bioc/html/EGSEA.html | -Transcriptomics, RNA, Statistics | -egsea | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea | -
- | emboss_5 | -5.0.0 | -6.6.0 | -emboss | -To update | -emboss | -EMBOSS | -Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment | -Molecular biology, Sequence analysis, Biology | -Galaxy wrappers for EMBOSS version 5.0.0 tools | -Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. | -- | To update | -http://emboss.open-bio.org/ | -Sequence Analysis, Fasta Manipulation | -emboss_5 | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 | -
- | ena_upload | -0.6.3 | -0.7.1 | -ena-upload-cli | -To update | -- | - | - | - | Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). | -- | - | To update | -https://github.com/usegalaxy-eu/ena-upload-cli | -Data Export | -ena_upload | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload | -
- | enasearch | -- | 0.2.2 | -enasearch | -To update | -- | - | - | - | A Python library for interacting with ENA's API | -- | - | To update | -https://github.com/bebatut/enasearch | -Data Source | -enasearch | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch | -
- | ensembl_vep | -110.1 | -111.0 | -ensembl-vep | -To update | -- | - | - | - | Ensembl VEP: Annotate VCFs with variant effect predictions | -- | - | To update | -https://github.com/Ensembl/ensembl-vep | -Variant Analysis | -ensembl_vep | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep | -
- | episcanpy | -0.3.2 | -0.4.0 | -episcanpy | -To update | -episcanpy | -epiScanpy | -Enrichment analysis, Imputation | -Epigenomics, Cell biology, DNA | -EpiScanpy – Epigenomics single cell analysis in python | -Epigenomics Single Cell Analysis in Python. | -- | To update | -https://github.com/colomemaria/epiScanpy | -Epigenetics | -episcanpy | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ | -
- | exomedepth | -1.1.0 | -1.1.16 | -r-exomedepth | -To update | -exomedepth | -ExomeDepth | -Sequence analysis, Variant calling, Genotyping, Copy number estimation | -Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases | -ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data | -Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. | -- | To update | -https://cran.r-project.org/package=ExomeDepth | -Sequence Analysis, Variant Analysis | -exomedepth | -crs4 | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth | -
- | exonerate | -2.4.0 | -2.4.0 | -exonerate | -Up-to-date | -exonerate | -Exonerate | -Pairwise sequence alignment, Protein threading, Genome alignment | -Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks | -Exonerate is a generic tool for pairwise sequence comparison. | -A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. | -- | Up-to-date | -https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate | -Sequence Analysis | -exonerate | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate | -
- | export2graphlan | -0.20 | -0.22 | -export2graphlan | -To update | -export2graphlan | -export2graphlan | -Conversion | -Taxonomy, Metabolomics, Biomarkers | -export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn | -export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. | -- | To update | -https://bitbucket.org/CibioCM/export2graphlan/overview | -Metagenomics | -export2graphlan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ | -
- | extract_genomic_dna | -3.0.3+galaxy2 | -0.11.0 | -bx-python | -To update | -- | - | - | - | Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. | -- | - | To update | -- | Genomic Interval Operations | -extract_genomic_dna | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna | -
- | fargene | -0.1 | -0.1 | -fargene | -Up-to-date | -fargene | -fARGene | -Antimicrobial resistance prediction | -Metagenomics, Microbiology, Public health and epidemiology | -fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) | -fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. | -- | Up-to-date | -https://github.com/fannyhb/fargene | -Sequence Analysis | -fargene | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene | -
- | fasta_nucleotide_color_plot | -1.0.1 | -- | openjdk | -To update | -- | - | - | - | Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. | -- | - | To update | -https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot | -Visualization | -fasta_nucleotide_color_plot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot | -
- | fasta_stats | -2.0 | -- | numpy | -To update | -- | - | - | - | Display summary statistics for a fasta file. | -- | - | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ | -Sequence Analysis | -fasta_stats | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ | -
- | fastani | -1.3 | -1.34 | -fastani | -To update | -- | - | - | - | Fast alignment-free computation of whole-genome Average Nucleotide Identity | -- | - | To update | -https://github.com/ParBLiSS/FastANI | -Sequence Analysis | -fastani | -iuc | -- |
- | fastp | -- | 0.23.4 | -fastp | -To update | -\n fastp\n | -- | - | - | Fast all-in-one preprocessing for FASTQ files | -- | - | To update | -https://github.com/OpenGene/fastp | -Sequence Analysis | -fastp | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp | -
- | fastqc | -0.74+galaxy0 | -0.12.1 | -fastqc | -To update | -fastqc | -FastQC | -Sequence composition calculation, Sequencing quality control, Statistical calculation | -Sequencing, Data quality management, Sequence analysis | -Read QC reports using FastQC | -This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. | -- | To update | -http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | -Fastq Manipulation | -fastqc | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc | -
- | fastqe | -0.3.1+galaxy0 | -0.3.1 | -fastqe | -To update | -fastqe | -FASTQE | -Sequencing quality control | -Sequence analysis, Sequencing | -FASTQE | -Compute quality stats for FASTQ files and print those stats as emoji... for some reason. | -- | To update | -https://fastqe.com/ | -Sequence Analysis | -fastqe | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe | -
- | fasttree | -2.1.10 | -2.1.11 | -fasttree | -To update | -fasttree | -FastTree | -Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) | -Phylogenetics, Sequence analysis | -FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL | -Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. | -- | To update | -http://www.microbesonline.org/fasttree/ | -Phylogenetics | -fasttree | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree | -
- | featurecounts | -2.0.3 | -2.0.6 | -subread | -To update | -featurecounts | -FeatureCounts | -Read summarisation | -Sequencing | -featureCounts counts the number of reads aligned to defined masked regions in a reference genome | -featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. | -- | To update | -http://bioinf.wehi.edu.au/featureCounts | -RNA, Transcriptomics, Sequence Analysis | -featurecounts | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts | -
- | feelnc | -0.2.1 | -0.2 | -feelnc | -To update | -feelnc | -FEELnc | -Annotation, Classification | -RNA-seq, Functional, regulatory and non-coding RNA | -Galaxy wrapper for FEELnc | -A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. | -- | To update | -https://github.com/tderrien/FEELnc | -Sequence Analysis | -feelnc | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc | -
- | fermikit | -r193 | -r193 | -fermi2 | -Up-to-date | -- | - | - | - | FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. | -- | - | Up-to-date | -https://github.com/lh3/fermikit | -Assembly, Variant Analysis | -fermikit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit | -
- | fgsea | -1.8.0+galaxy1 | -1.28.0 | -bioconductor-fgsea | -To update | -fgsea | -fgsea | -Gene-set enrichment analysis | -Genetics | -Perform gene set testing using fgsea | -The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. | -- | To update | -https://bioconductor.org/packages/release/bioc/html/fgsea.html | -Visualization, Transcriptomics, Statistics | -fgsea | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea | -
- | filtlong | -0.2.1 | -0.2.1 | -filtlong | -Up-to-date | -\n filtlong\n | -- | - | - | Filtlong - Filtering long reads by quality | -- | - | Up-to-date | -https://github.com/rrwick/Filtlong | -Fastq Manipulation, Sequence Analysis | -filtlong | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong | -
- | flair | -1.5 | -2.0.0 | -flair | -To update | -- | - | - | - | FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. | -- | - | To update | -https://github.com/BrooksLabUCSC/flair | -Nanopore | -flair | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair | -
- | flash | -1.2.11 | -1.2.11 | -flash | -Up-to-date | -flash | -FLASH | -Read pre-processing, Sequence merging, Sequence assembly | -Sequencing, Sequence assembly | -Fast Length Adjustment of SHort reads | -Identifies paired-end reads which overlap in the middle, converting them to single long reads | -- | Up-to-date | -https://ccb.jhu.edu/software/FLASH/ | -Assembly, Fastq Manipulation | -flash | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash | -
- | fraggenescan | -- | 1.31 | -fraggenescan | -To update | -fraggenescan | -FragGeneScan | -Gene prediction | -Genetics, Sequence analysis | -Tool for finding (fragmented) genes in short read | -Application for finding (fragmented) genes in short reads | -- | To update | -https://sourceforge.net/projects/fraggenescan/ | -Sequence Analysis | -fraggenescan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ | -
- | freebayes | -1.3.6 | -1.3.7 | -freebayes | -To update | -freebayes | -FreeBayes | -Variant calling, Statistical calculation | -Genomics, Genetic variation, Rare diseases | -Galaxy Freebayes Bayesian genetic variant detector tool | -Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. | -- | To update | -https://github.com/ekg/freebayes | -Variant Analysis | -freebayes | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes | -
- | freec | -11.6 | -- | gawk | -To update | -freec | -FREEC | -Copy number estimation, Variant calling, Genome alignment | -DNA structural variation, Oncology, Human genetics, Data mining | -Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. | -A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. | -- | To update | -http://boevalab.inf.ethz.ch/FREEC/ | -Variant Analysis | -control_freec | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec | -
- | freyja | -1.4.4 | -1.4.9 | -freyja | -To update | -freyja | -- | - | - | lineage abundances estimation | -- | - | To update | -https://github.com/andersen-lab/Freyja | -Metagenomics, Sequence Analysis | -freyja | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja | -
- | fsd | -1.0.2 | -- | matplotlib | -To update | -- | - | - | - | Tool that plots a histogram of sizes of read families | -- | - | To update | -- | Graphics | -duplex_family_size_distribution | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd | -
- | funannotate | -1.8.15 | -- | - | To update | -\n funannotate\n | -- | - | - | Funannotate is a genome prediction, annotation, and comparison software package. | -- | - | To update | -https://funannotate.readthedocs.io | -Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate | -
- | gatk4 | -4.1.7.0 | -4.5.0.0 | -gatk4 | -To update | -- | - | - | - | A Galaxy wrapper for Mutect2 from GATK | -- | - | To update | -https://software.broadinstitute.org/gatk/gatk4 | -Variant Analysis | -gatk4_mutect2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 | -
- | gdcwebapp | -1.0.0 | -- | python | -To update | -- | - | - | - | GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format | -- | - | To update | -http://bioinf.iasi.cnr.it/gdcwebapp/ | -Data Source, Convert Formats | -gdcwebapp | -iuc | -https://github.com/fabio-cumbo/GDCWebApp4Galaxy | -
- | gecko | -1.2 | -1.2 | -gecko | -Up-to-date | -- | - | - | - | Ungapped genome comparison | -- | - | Up-to-date | -https://github.com/otorreno/gecko | -Sequence Analysis | -gecko | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko | -
- | gemini | -0.20.1 | -0.30.2 | -gemini | -To update | -gemini | -GEMINI | -Sequence analysis, Genetic variation analysis | -Sequence analysis | -GEMINI: a flexible framework for exploring genome variation | -GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. | -- | To update | -https://github.com/arq5x/gemini | -Sequence Analysis, Next Gen Mappers | -gemini | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini | -
- | genebed_maf_to_fasta | -1.0.1+galaxy0 | -- | - | To update | -- | - | - | - | Stitch gene blocks given a set of coding exon intervals | -- | - | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ | -Genomic Interval Operations | -genebed_maf_to_fasta | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ | -
- | genehunter_modscore | -3.0.0 | -3.1 | -ghm | -To update | -- | - | - | - | Maximised LOD score pedigree analysis utility | -- | - | To update | -https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html | -Variant Analysis | -genehunter_modscore | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ | -
- | geneiobio | -4.7.1+galaxy1 | -- | - | To update | -- | - | - | - | Gene.iobio is an interactive tool for variant and trio analysis. | -- | - | To update | -https://github.com/iobio/gene.iobio | -Sequence Analysis | -geneiobio | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio | -
- | genetrack | -- | - | numpy | -To update | -- | - | - | - | Contains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand. | -- | - | To update | -- | ChIP-seq | -genetrack | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack | -
- | genomescope | -2.0 | -2.0 | -genomescope2 | -Up-to-date | -- | - | - | - | Analyze unassembled short reads | -- | - | Up-to-date | -https://github.com/tbenavi1/genomescope2.0 | -Statistics | -genomescope | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope | -
- | genomic_super_signature | -1.2.0 | -1.10.0 | -bioconductor-genomicsupersignature | -To update | -genomicsupersignature | -GenomicSuperSignature | -Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction | -RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment | -Interpretation of RNAseq experiments through robust, efficient comparison to public databases | -GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. | -- | To update | -https://github.com/shbrief/GenomicSuperSignature | -Sequence Analysis, RNA, Transcriptomics | -genomic_super_signature | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature | -
- | genrich | -0.5+galaxy2 | -0.6.1 | -genrich | -To update | -- | - | - | - | Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). | -- | - | To update | -https://github.com/jsh58/Genrich | -ChIP-seq | -genrich | -iuc | -https://github.com/jsh58/Genrich | -
- | get_hrun | -0.5.9.2 | -0.8.1.1 | -pyfaidx | -To update | -- | - | - | - | Annotate indel variants with homopolymer context | -- | - | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun | -Variant Analysis | -get_hrun | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun | -
- | getorganelle | -1.7.7.0 | -1.7.7.0 | -getorganelle | -Up-to-date | -getorganelle | -GetOrganelle | -De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming | -Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms | -GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. | -A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. | -- | Up-to-date | -https://github.com/Kinggerm/GetOrganelle | -Assembly | -getorganelle | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle | -
- | gfa_to_fa | -0.1.2 | -- | - | To update | -- | - | - | - | gfa_to_fa - Converting GFA format to Fasta format | -- | - | To update | -http://gfa-spec.github.io/GFA-spec/ | -Convert Formats | -gfa_to_fa | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa | -
- | gff3_rebase | -1.2 | -0.6.6 | -bcbiogff | -To update | -- | - | - | - | Rebase a GFF against a parent GFF (e.g. an original genome) | -- | - | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase | -Sequence Analysis | -gff3_rebase | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase | -
- | gffcompare | -0.12.6 | -0.12.6 | -gffcompare | -Up-to-date | -gffcompare | -gffcompare | -Sequence annotation | -Nucleic acids, Sequence analysis | -Galaxy wrappers for Geo Pertea's GffCompare package. | -Program for comparing, annotating, merging and tracking transcripts in GFF files. | -- | Up-to-date | -https://github.com/gpertea/gffcompare/ | -Transcriptomics | -gffcompare | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare | -
- | gffread | -0.12.7 | -0.12.7 | -gffread | -Up-to-date | -gffread | -gffread | -Sequence annotation | -Nucleic acids, Sequence analysis | -gffread filters and/or converts GFF3/GTF2 records | -program for filtering, converting and manipulating GFF files | -- | Up-to-date | -http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ | -Sequence Analysis | -gffread | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread | -
- | ggplot2 | -3.4.0 | -- | r-base | -To update | -ggplot2 | -ggplot2 | -Visualisation | -Data visualisation | -ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. | -Plotting system for R, based on the grammar of graphics. | -- | To update | -https://github.com/tidyverse/ggplot2 | -Visualization | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 | -
- | ggupset | -1.0 | -- | r-ggupset | -To update | -- | - | - | - | Create Upset Plots with ggupset | -- | - | To update | -https://github.com/const-ae/ggupset | -Graphics | -ggupset | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset | -
- | glimmer | -- | 3.02 | -glimmer | -To update | -gemini | -GEMINI | -Sequence analysis, Genetic variation analysis | -Sequence analysis | -Glimmer makes gene predictions. | -GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. | -- | To update | -https://ccb.jhu.edu/software/glimmer/ | -Sequence Analysis | -- | bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer | -
- | goenrichment | -2.0.1 | -2.0.1 | -goenrichment | -Up-to-date | -goenrichment | -GOEnrichment | -Gene-set enrichment analysis | -Transcriptomics | -Performs GO Enrichment analysis. | -GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de CiĂŞncia. | -- | Up-to-date | -https://github.com/DanFaria/GOEnrichment | -Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment | -
- | goseq | -1.50.0 | -1.54.0 | -bioconductor-goseq | -To update | -goseq | -GOseq | -Gene functional annotation | -RNA-Seq | -goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data | -Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. | -- | To update | -https://bioconductor.org/packages/release/bioc/html/goseq.html | -Statistics, RNA, Micro-array Analysis | -goseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq | -
- | gprofiler | -@TOOL_VERSION@+galaxy11 | -- | r-gprofiler2 | -To update | -- | - | - | - | functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more | -- | - | To update | -https://biit.cs.ut.ee/gprofiler | -Statistics, Web Services | -gprofiler | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ | -
- | graphembed | -2.4 | -2.4 | -graph_embed | -Up-to-date | -- | - | - | - | Compute a 2D embedding of a data matrix given supervised class information | -- | - | Up-to-date | -https://github.com/fabriziocosta/GraphEmbed | -Statistics, Graphics | -graphembed | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ | -
- | graphlan | -- | 1.1.3 | -graphlan | -To update | -graphlan | -GraPhlAn | -Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification | -Metagenomics, Phylogenetics, Phylogenomics, Cladistics | -GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees | -GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. | -- | To update | -https://github.com/biobakery/graphlan | -Metagenomics, Graphics, Phylogenetics | -graphlan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ | -
- | gtdbtk | -2.3.2 | -2.3.2 | -gtdbtk | -Up-to-date | -GTDB-Tk | -GTDB-Tk | -Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval | -Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins | -GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. | -a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). | -- | Up-to-date | -https://github.com/Ecogenomics/GTDBTk | -Metagenomics | -gtdbtk | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk | -
- | gtfToBed12 | -357 | -447 | -ucsc-gtftogenepred | -To update | -UCSC_Genome_Browser_Utilities | -UCSC Genome Browser Utilities | -- | Sequence analysis | -Convert GTF files to BED12 format | -Utilities for handling sequences and assemblies from the UCSC Genome Browser project. | -- | To update | -http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README | -Convert Formats | -gtftobed12 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 | -
- | gubbins | -3.2.1 | -3.3.3 | -gubbins | -To update | -gubbins | -Gubbins | -Genotyping, Phylogenetic inference, Ancestral reconstruction | -Phylogeny, Genotype and phenotype, Whole genome sequencing | -Gubbins - bacterial recombination detection | -Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. | -- | To update | -- | Sequence Analysis | -gubbins | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins | -
- | gvcftools | -0.1 | -0.17.0 | -gvcftools | -To update | -- | - | - | - | - | - | - | To update | -https://github.com/sequencing/gvcftools | -Variant Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools | -
- | gwastools | -0.1.0 | -1.48.0 | -bioconductor-gwastools | -To update | -gwastools | -GWASTools | -Deposition, Analysis, Annotation | -GWAS study | -- | Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. | -- | To update | -https://bioconductor.org/packages/release/bioc/html/GWASTools.html | -Visualization, Variant Analysis | -- | iuc | -- |
- | hamronization | -1.0.3 | -1.1.4 | -hamronization | -To update | -hamronization | -hAMRonization | -Data handling, Antimicrobial resistance prediction, Parsing | -Public health and epidemiology, Microbiology, Bioinformatics | -Convert AMR gene detection tool output to hAMRonization specification format. | -Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure | -- | To update | -https://github.com/pha4ge/hAMRonization | -Sequence Analysis | -hamronization | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization | -
- | hansel | -2.6.1 | -2.6.1 | -bio_hansel | -Up-to-date | -Biohansel | -BioHansel | -Genotyping, SNP detection, Genome assembly | -Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science | -Heidelberg and Enteritidis SNP Elucidation | -BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. | -- | Up-to-date | -https://github.com/phac-nml/bio_hansel | -Sequence Analysis | -bio_hansel | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel | -
- | hapcut2 | -1.3.3 | -1.3.3 | -hapcut2 | -Up-to-date | -hapcut2 | -HapCUT2 | -Haplotype mapping, Variant classification | -- | Robust and accurate haplotype assembly for diverse sequencing technologies | -HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md | -- | Up-to-date | -https://github.com/vibansal/HapCUT2 | -Assembly | -hapcut2 | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc | -
- | hapog | -1.3.7 | -1.3.7 | -hapog | -Up-to-date | -hapog | -Hapo-G | -Genome assembly, Optimisation and refinement | -Sequence assembly, Genomics | -Hapo-G - Haplotype-Aware Polishing of Genomes | -Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. | -- | Up-to-date | -https://github.com/institut-de-genomique/HAPO-G | -Assembly | -hapog | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog | -
- | happy | -0.3.14 | -0.3.15 | -hap.py | -To update | -hap.py | -hap.py | -Variant calling, Sequence analysis, Genotyping | -Genomics, DNA polymorphism | -A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. | -This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. | -- | To update | -https://github.com/Illumina/hap.py | -Variant Analysis | -happy | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy | -
- | heatmap2 | -3.1.3.1 | -2.17.0 | -r-gplots | -To update | -- | - | - | - | heatmap.2 function from the R gplots package | -- | - | To update | -https://github.com/cran/gplots | -Visualization | -ggplot2_heatmap2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 | -
- | heinz | -1.0 | -1.62.0 | -bioconductor-bionet | -To update | -bionet | -BioNet | -Protein interaction analysis | -Molecular interactions, pathways and networks, Protein interactions | -An algorithm for identification of the optimal scoring subnetwork. | -This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork. | -- | To update | -https://github.com/ls-cwi/heinz | -Transcriptomics, Visualization, Statistics | -heinz | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz | -
- | hicexplorer | -3.7.2 | -3.7.3 | -hicexplorer | -To update | -- | - | - | - | HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. | -- | - | To update | -https://github.com/deeptools/HiCExplorer | -Sequence Analysis, Visualization | -hicexplorer | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer | -
- | hicstuff | -3.1.5 | -3.2.2 | -hicstuff | -To update | -- | - | - | - | - | - | - | To update | -https://github.com/koszullab/hicstuff | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff | -
- | hifiasm_meta | -0.3.1 | -hamtv0.3.1 | -hifiasm_meta | -To update | -hifiasm-meta | -Hifiasm-meta | -Sequence assembly | -Sequence assembly, Metagenomics | -A hifiasm fork for metagenome assembly using Hifi reads. | -Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. | -- | To update | -https://github.com/xfengnefx/hifiasm-meta | -Metagenomics | -hifiasm_meta | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta | -
- | hisat2 | -2.2.1 | -2.2.1 | -hisat2 | -Up-to-date | -hisat2 | -HISAT2 | -Sequence alignment | -RNA-seq | -HISAT2 is a fast and sensitive spliced alignment program. | -Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). | -- | Up-to-date | -http://ccb.jhu.edu/software/hisat2/ | -Assembly | -hisat2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 | -
- | hivclustering | -1.3.1 | -1.6.8 | -python-hivclustering | -To update | -- | - | - | - | Infers transmission networks from pairwise distances inferred by tn93 | -- | - | To update | -https://pypi.org/project/hivclustering/ | -Next Gen Mappers | -hivclustering | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ | -
- | hmmer3 | -3.4 | -3.4 | -hmmer | -Up-to-date | -hmmer3 | -HMMER3 | -Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search | -Sequence analysis, Sequence sites, features and motifs, Gene and protein families | -HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). | -This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. | -- | Up-to-date | -http://hmmer.org/ | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 | -
- | homer | -4.11 | -4.11 | -homer | -Up-to-date | -homer | -homer | -Sequence motif discovery | -- | HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. | -HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. | -- | Up-to-date | -http://homer.ucsd.edu/homer/index.html | -Sequence Analysis | -data_manager_homer_preparse | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer | -
- | htseq_count | -2.0.5 | -2.0.5 | -htseq | -Up-to-date | -htseq | -HTSeq | -Nucleic acid sequence analysis | -Sequence analysis | -Count aligned reads (SAM/BAM) that overlap genomic features (GFF) | -Python framework to process and analyse high-throughput sequencing (HTS) data | -- | Up-to-date | -https://readthedocs.org/projects/htseq/ | -Genomic Interval Operations, SAM, Sequence Analysis, RNA | -htseq_count | -lparsons | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count | -
- | humann | -3.8 | -3.8 | -humann | -Up-to-date | -humann | -humann | -Species frequency estimation, Taxonomic classification, Phylogenetic analysis | -Metagenomics, Phylogenomics | -HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution | -HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” | -- | Up-to-date | -http://huttenhower.sph.harvard.edu/humann | -Metagenomics | -humann | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann | -
- | hybpiper | -2.1.6 | -2.1.6 | -hybpiper | -Up-to-date | -HybPiper | -HybPiper | -Sequence trimming, Sequence assembly, Read mapping | -Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics | -Analyse targeted sequence capture data | -Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. | -- | Up-to-date | -https://github.com/mossmatters/HybPiper | -Sequence Analysis, Phylogenetics | -hybpiper | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper | -
- | hyphy | -2.5.47 | -2.5.59 | -hyphy | -To update | -HyPhy | -HyPhy | -Statistical calculation | -Phylogeny, Small molecules, Molecular interactions, pathways and networks | -Hypothesis Testing using Phylogenies | -Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. | -- | To update | -http://www.hyphy.org | -Phylogenetics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ | -
- | hypo | -1.0.3 | -1.0.3 | -hypo | -Up-to-date | -HyPo | -HyPo | -Optimisation and refinement, Genome assembly | -Sequence assembly, Genomics | -Super Fast & Accurate Polisher for Long Read Genome Assemblies | -HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. | -- | Up-to-date | -https://github.com/kensung-lab/hypo | -Assembly | -hypo | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo | -
- | icescreen | -1.3.1 | -1.3.2 | -icescreen | -To update | -icescreen | -ICEscreen | -Database search, Protein feature detection | -Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation | -ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. | -A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. | -- | To update | -https://icescreen.migale.inrae.fr/ | -Genome annotation | -icescreen | -iuc | -https://forgemia.inra.fr/ices_imes_analysis/icescreen | -
- | idba_ud | -- | 1.1.3 | -idba | -To update | -idba | -IDBA | -Sequence assembly | -Sequence assembly | -Wrappers for the idba assembler variants. | -A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. | -- | To update | -https://i.cs.hku.hk/~alse/hkubrg/projects/index.html | -Assembly | -idba | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud | -
- | idr | -2.0.3 | -2.0.4.2 | -idr | -To update | -- | - | - | - | Galaxy wrappers for the IDR package from Nathan Boleu | -- | - | To update | -https://github.com/nboley/idr | -Sequence Analysis | -idr | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ | -
- | idr_download | -0.44.1 | -5.11.1 | -omero-py | -To update | -- | - | - | - | Image Data Resource downloading tool | -- | - | To update | -https://idr.openmicroscopy.org | -Data Source | -idr_download_by_ids | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download | -
- | iedb_api | -2.15.2 | -- | python | -To update | -- | - | - | - | Get epitope binding predictions from IEDB-API | -- | - | To update | -http://tools.immuneepitope.org/main/tools-api/ | -Data Source, Sequence Analysis | -iedb_api | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api | -
- | instrain | -1.5.3 | -1.8.0 | -instrain | -To update | -instrain | -InStrain | -SNP detection, Genome comparison | -Mapping, Metagenomics | -InStrain is a tool for analysis of co-occurring genome populations from metagenomes | -InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification | -- | To update | -https://instrain.readthedocs.io/en/latest/# | -Metagenomics | -instrain | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain | -
- | integron_finder | -2.0.3 | -2.0.3 | -integron_finder | -Up-to-date | -integron_finder | -Integron Finder | -Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation | -Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis | -"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching" | -A tool to detect Integron in DNA sequences. | -- | Up-to-date | -https://github.com/gem-pasteur/Integron_Finder | -Sequence Analysis | -integronfinder | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder | -
- | intermine_galaxy_exchange | -0.0.1 | -8.25 | -coreutils | -To update | -- | - | - | - | InterMine Exporter | -- | - | To update | -- | Convert Formats | -intermine_galaxy_exchange | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange | -
- | interproscan | -5.59-91.0 | -- | interproscan | -To update | -interproscan_ebi | -InterProScan (EBI) | -Sequence motif recognition, Protein feature detection | -Gene and protein families, Sequence analysis | -Interproscan queries the interpro database and provides annotations. | -Scan sequences against the InterPro protein signature databases. | -- | To update | -http://www.ebi.ac.uk/Tools/pfa/iprscan5/ | -Sequence Analysis | -interproscan | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan | -
- | interval2maf | -1.0.1+galaxy1 | -0.11.0 | -bx-python | -To update | -bx-python | -bx-python | -- | Sequence analysis | -Extract MAF blocks given a set of intervals | -Tools for manipulating biological data, particularly multiple sequence alignments. | -- | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ | -Genomic Interval Operations | -interval2maf | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ | -
- | intervene | -0.6.5 | -0.6.5 | -intervene | -Up-to-date | -intervene | -Intervene | -Sequence comparison, Sequence visualisation | -Computational biology | -Create pairwise and upset plots | -Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. | -- | Up-to-date | -https://intervene.readthedocs.io | -Statistics | -intervene | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene | -
- | iqtree | -2.1.2 | -2.2.6 | -iqtree | -To update | -- | - | - | - | Efficient phylogenomic software by maximum likelihood | -- | - | To update | -http://www.iqtree.org/ | -Phylogenetics | -iqtree | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ | -
- | irissv | -1.0.4 | -1.19.2 | -samtools | -To update | -- | - | - | - | Refine insertion sequences | -- | - | To update | -https://github.com/mkirsche/Iris | -Variant Analysis | -irissv | -iuc | -https://github.com/galaxyproject/tools-iuc/tools/irissv/ | -
- | isescan | -1.7.2.3 | -1.7.2.1 | -isescan | -To update | -ISEScan | -ISEScan | -Structural variation detection | -Genomics, DNA structural variation, Sequence analysis, Genetic variation | -"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements." | -Automated identification of insertion sequence elements in prokaryotic genomes. | -- | To update | -https://github.com/xiezhq/ISEScan | -Sequence Analysis | -ISEScan | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan | -
- | isoformswitchanalyzer | -1.20.0 | -2.2.0 | -bioconductor-isoformswitchanalyzer | -To update | -IsoformSwitchAnalyzeR | -IsoformSwitchAnalyzeR | -Sequence comparison, Sequence analysis | -Computational biology, Gene transcripts | -Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. | -Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. | -- | To update | -https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html | -Transcriptomics, RNA, Statistics | -isoformswitchanalyzer | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer | -
- | ivar | -1.4.2 | -1.4.2 | -ivar | -Up-to-date | -- | - | - | - | iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing | -- | - | Up-to-date | -https://github.com/andersen-lab/ivar | -Sequence Analysis | -ivar | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ | -
- | iwtomics | -1.0.0 | -1.26.0 | -bioconductor-iwtomics | -To update | -iwtomics | -IWTomics | -Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison | -Statistics and probability | -Interval-Wise Testing for Omics Data | -Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset. | -- | To update | -https://bioconductor.org/packages/release/bioc/html/IWTomics.html | -Statistics | -iwtomics | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics | -
- | jasminesv | -1.0.11 | -1.1.5 | -jasminesv | -To update | -- | - | - | - | Merge structural variants across samples | -- | - | To update | -https://github.com/mkirsche/Jasmine/ | -Variant Analysis | -jasminesv | -iuc | -https://github.com/galaxyproject/tools-iuc/jasminesv/ | -
- | jbrowse | -1.16.11 | -1.16.11 | -jbrowse | -Up-to-date | -jbrowse | -JBrowse | -Genome visualisation | -Genomics | -JBrowse Genome Browser integrated as a Galaxy Tool | -Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. | -- | Up-to-date | -https://jbrowse.org | -Sequence Analysis | -jbrowse | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse | -
- | jcvi_gff_stats | -0.8.4 | -1.3.9 | -jcvi | -To update | -- | - | - | - | Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) | -- | - | To update | -https://github.com/tanghaibao/jcvi | -Sequence Analysis | -jcvi_gff_stats | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats | -
- | jellyfish | -- | 2.3.1 | -kmer-jellyfish | -To update | -Jellyfish | -Jellyfish | -k-mer counting | -Sequence analysis, Genomics | -Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA | -A command-line algorithm for counting k-mers in DNA sequence. | -- | To update | -https://github.com/gmarcais/Jellyfish | -Assembly | -jellyfish | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish | -
- | join_files_by_id | -1.0 | -1.11.6 | -r-data.table | -To update | -- | - | - | - | This tool will join datasets according to a column with identifier | -- | - | To update | -- | Text Manipulation | -join_files_by_id | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id | -
- | jq | -1.0 | -1.5 | -jq | -To update | -- | - | - | - | JQ is a lightweight and flexible command-line JSON processor | -- | - | To update | -https://stedolan.github.io/jq/ | -Text Manipulation | -jq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq | -
- | jvarkit | -20201223 | -20201223 | -jvarkit-wgscoverageplotter | -Up-to-date | -- | - | - | - | Jvarkit : Java utilities for Bioinformatics | -- | - | Up-to-date | -https://lindenb.github.io/jvarkit/ | -SAM | -jvarkit | -iuc | -https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit | -
- | kallisto | -0.48.0 | -0.50.1 | -kallisto | -To update | -kallisto | -kallisto | -Gene expression profiling | -Transcriptomics, RNA-seq, Gene expression | -kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. | -A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. | -- | To update | -https://pachterlab.github.io/kallisto/ | -Transcriptomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ | -
- | kc-align | -1.0.2 | -1.0.2 | -kcalign | -Up-to-date | -kc-align | -kc-align | -Multiple sequence alignment | -Mapping | -Kc-Align custom tool | -A fast and accurate tool for performing codon-aware multiple sequence alignments | -- | Up-to-date | -https://github.com/davebx/kc-align | -Sequence Analysis | -kc_align | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align | -
- | khmer | -3.0.0a3 | -3.0.0a3 | -khmer | -Up-to-date | -khmer | -khmer | -Standardisation and normalisation, De-novo assembly | -Sequence assembly | -In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more | -khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. | -- | Up-to-date | -https://khmer.readthedocs.org/ | -Assembly, Next Gen Mappers | -khmer | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer | -
- | king | -2.2.7 | -2.2.7 | -king | -Up-to-date | -- | - | - | - | Kinship-based INference for Gwas | -- | - | Up-to-date | -http://people.virginia.edu/~wc9c/KING/ | -Variant Analysis | -king | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ | -
- | kleborate | -2.3.2 | -2.3.2 | -kleborate | -Up-to-date | -kleborate | -Kleborate | -Multilocus sequence typing, Genome assembly, Virulence prediction | -Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing | -Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) | -Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). | -- | Up-to-date | -https://github.com/katholt/Kleborate/wiki | -Metagenomics | -kleborate | -iuc | -https://github.com/katholt/Kleborate | -
- | kma | -1.2.21 | -1.4.14 | -kma | -To update | -- | - | - | - | Map with KMA | -- | - | To update | -https://bitbucket.org/genomicepidemiology/kma | -Next Gen Mappers | -kma | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma | -
- | kofamscan | -1.3.0 | -1.3.0 | -kofamscan | -Up-to-date | -- | - | - | - | Gene function annotation tool based on KEGG Orthology and hidden Markov model | -- | - | Up-to-date | -https://github.com/takaram/kofam_scan | -Sequence Analysis | -kofamscan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan | -
- | kraken_biom | -1.2.0 | -1.2.0 | -kraken-biom | -Up-to-date | -- | - | - | - | Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) | -- | - | Up-to-date | -https://github.com/smdabdoub/kraken-biom | -Metagenomics | -kraken_biom | -iuc | -https://github.com/smdabdoub/kraken-biom | -
- | kraken_taxonomy_report | -0.0.3 | -1.70 | -biopython | -To update | -- | - | - | - | Kraken taxonomy report | -- | - | To update | -https://github.com/blankenberg/Kraken-Taxonomy-Report | -Metagenomics | -kraken_taxonomy_report | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report | -
- | krakentools | -1.2 | -1.2 | -krakentools | -Up-to-date | -krakentools | -KrakenTools | -Visualisation, Aggregation | -Taxonomy, Metagenomics | -KrakenTools is a suite of scripts to be used alongside the Kraken | -KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files | -- | Up-to-date | -https://github.com/jenniferlu717/KrakenTools | -Metagenomics | -krakentools | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools | -
- | krocus | -1.0.1 | -1.0.3 | -krocus | -To update | -- | - | - | - | Predict MLST directly from uncorrected long reads | -- | - | To update | -https://github.com/quadram-institute-bioscience/krocus | -Sequence Analysis | -krocus | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus | -
- | last | -1205 | -1542 | -last | -To update | -last | -LAST | -Sequence alignment | -Genomics, Comparative genomics | -LAST finds similar regions between sequences. | -Short read alignment program incorporating quality scores | -- | To update | -http://last.cbrc.jp/ | -Sequence Analysis | -last | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/last | -
- | lastz | -1.04.22 | -1.04.22 | -lastz | -Up-to-date | -lastz | -LASTZ | -Sequence alignment, Read mapping | -Genomics | -Galaxy wrappers for the Lastz and Lastz_d | -A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. | -- | Up-to-date | -https://github.com/lastz/lastz | -Next Gen Mappers | -lastz | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz | -
- | lcrgenie | -1.0.2 | -- | lcr_genie | -To update | -- | - | - | - | Ligase Chain Reaction Genie | -- | - | To update | -https://github.com/neilswainston/LCRGenie | -Synthetic Biology | -lcrgenie | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie | -
- | legsta | -0.5.1 | -0.5.1 | -legsta | -Up-to-date | -- | - | - | - | Performs in silico Legionella pneumophila sequence based typing. | -- | - | Up-to-date | -https://github.com/tseemann/legsta | -Sequence Analysis | -legsta | -iuc | -https://github.com/tseemann/legsta | -
- | length_and_gc_content | -0.1.2 | -1.3.2 | -r-optparse | -To update | -- | - | - | - | Gets gene length and gc content from a fasta and a GTF file | -- | - | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content | -Fasta Manipulation, Statistics, RNA, Micro-array Analysis | -length_and_gc_content | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content | -
- | limma_voom | -3.58.1 | -3.58.1 | -bioconductor-limma | -Up-to-date | -limma | -limma | -RNA-Seq analysis | -Molecular biology, Genetics | -Perform RNA-Seq differential expression analysis using limma voom pipeline | -Data analysis, linear models and differential expression for microarray data. | -- | Up-to-date | -http://bioconductor.org/packages/release/bioc/html/limma.html | -Transcriptomics, RNA, Statistics | -limma_voom | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom | -
- | lineagespot | -1.6.0 | -- | r-base | -To update | -lineagespot | -lineagespot | -Variant calling | -Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation | -Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) | -Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). | -- | To update | -https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html | -Metagenomics, Sequence Analysis | -lineagespot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot | -
- | links | -2.0.1 | -2.0.1 | -links | -Up-to-date | -links | -LINKS | -Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming | -Sequence assembly, Mapping, Sequencing | -Scaffold genome assemblies with long reads. | -LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. | -- | Up-to-date | -https://github.com/bcgsc/LINKS | -Assembly | -links | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/links | -
- | lofreq | -2.1.5 | -2.1.5 | -lofreq | -Up-to-date | -- | - | - | - | LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. | -- | - | Up-to-date | -https://csb5.github.io/lofreq/ | -Variant Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq | -
- | lorikeet | -20 | -20 | -lorikeet | -Up-to-date | -- | - | - | - | Tools for M. tuberculosis DNA fingerprinting (spoligotyping) | -- | - | Up-to-date | -https://github.com/AbeelLab/lorikeet | -Sequence Analysis | -lorikeet_spoligotype | -iuc | -https://github.com/AbeelLab/lorikeet | -
- | lumpy_sv | -0.3.1 | -0.3.1 | -lumpy-sv | -Up-to-date | -- | - | - | - | LUMPY - a general probabilistic framework for structural variant discovery | -- | - | Up-to-date | -http://layerlab.org/software/ | -Variant Analysis | -lumpy_sv | -iuc | -https://github.com/arq5x/lumpy-sv | -
- | m6anet | -2.1.0 | -2.1.0 | -m6anet | -Up-to-date | -m6Anet | -m6Anet | -Quantification, Imputation, Gene expression profiling | -RNA-Seq, Transcriptomics, RNA, Machine learning | -m6anet to detect m6A RNA modifications from nanopore data | -Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. | -- | Up-to-date | -https://m6anet.readthedocs.io/en/latest | -Sequence Analysis | -m6anet | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet | -
- | maaslin2 | -0.99.12 | -0.99.12 | -maaslin2 | -Up-to-date | -- | - | - | - | MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. | -- | - | Up-to-date | -http://huttenhower.sph.harvard.edu/maaslin | -Metagenomics | -maaslin2 | -iuc | -https://github.com/biobakery/Maaslin2 | -
- | macs2 | -2.2.9.1 | -2.2.9.1 | -macs2 | -Up-to-date | -macs | -MACS | -Peak calling, Enrichment analysis, Gene regulatory network analysis | -ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites | -MACS - Model-based Analysis of ChIP-Seq | -Model-based Analysis of ChIP-seq data. | -- | Up-to-date | -https://github.com/taoliu/MACS | -Sequence Analysis, Statistics | -macs2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 | -
- | maf_stats | -1.0.2+galaxy0 | -- | - | To update | -- | - | - | - | MAF Coverage statistics | -- | - | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ | -Genomic Interval Operations | -maf_stats | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ | -
- | mageck | -0.5.9.2 | -0.5.9.5 | -mageck | -To update | -mageck | -MAGeCK | -Genetic variation analysis | -Genetics, Genetic variation, Genomics | -Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. | -Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. | -- | To update | -https://sourceforge.net/projects/mageck/ | -Genome editing | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck | -
- | maker | -2.31.11 | -3.01.03 | -maker | -To update | -maker | -MAKER | -Genome annotation | -Genomics, DNA, Sequence analysis | -MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. | -Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. | -- | To update | -http://www.yandell-lab.org/software/maker.html | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker | -
- | malt | -0.5.3 | -0.62 | -malt | -To update | -- | - | - | - | Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. | -- | - | To update | -https://github.com/husonlab/malt | -Next Gen Mappers | -malt_run | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt | -
- | map_param_value | -0.2.0 | -- | - | To update | -- | - | - | - | Map a parameter value to another value | -- | - | To update | -- | Text Manipulation | -map_param_value | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value | -
- | mapseq | -2.1.1 | -- | perl | -To update | -- | - | - | - | fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. | -- | - | To update | -https://github.com/jfmrod/MAPseq | -Metagenomics | -mapseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq | -
- | mash | -2.3 | -2.3 | -mash | -Up-to-date | -mash | -Mash | -Sequence distance matrix generation | -Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation | -Fast genome and metagenome distance estimation using MinHash | -Fast genome and metagenome distance estimation using MinHash. | -- | Up-to-date | -https://github.com/marbl/Mash | -Metagenomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash | -
- | mashmap | -3.1.3 | -3.1.3 | -mashmap | -Up-to-date | -- | - | - | - | Fast local alignment boundaries | -- | - | Up-to-date | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap | -Sequence Analysis | -mashmap | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap | -
- | masigpro | -1.49.3 | -8.25 | -coreutils | -To update | -masigpro | -maSigPro | -Regression analysis | -Gene expression, Molecular genetics, Microarray experiment, RNA-Seq | -Identify significantly differential expression profiles in time-course microarray experiments | -Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. | -- | To update | -https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html | -Transcriptomics, RNA, Statistics | -masigpro | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro | -
- | maxbin2 | -- | 2.2.7 | -maxbin2 | -To update | -maxbin | -MaxBin | -Sequence assembly | -Metagenomics, Sequence assembly, Microbiology | -clusters metagenomic contigs into bins | -Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. | -- | To update | -https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html | -Metagenomics | -maxbin2 | -mbernt | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ | -
- | mcl | -22.282 | -22.282 | -mcl | -Up-to-date | -mcl | -MCL | -Clustering, Network analysis, Gene regulatory network analysis | -Molecular interactions, pathways and networks | -The Markov Cluster Algorithm, a cluster algorithm for graphs | -MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. | -- | Up-to-date | -https://micans.org/mcl/man/mcl.html | -Sequence Analysis | -mcl | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/mcl | -
- | medaka | -1.7.2 | -1.11.3 | -medaka | -To update | -medaka | -Medaka | -Base-calling, Variant calling, Sequence assembly | -Sequence assembly, Machine learning | -Sequence correction provided by ONT Research | -medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. | -- | To update | -https://github.com/nanoporetech/medaka | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka | -
- | megahit | -1.2.9 | -1.2.9 | -megahit | -Up-to-date | -megahit | -MEGAHIT | -Genome assembly | -Metagenomics, Sequencing, Ecology, Sequence assembly | -An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. | -Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. | -- | Up-to-date | -https://github.com/voutcn/megahit | -Sequence Analysis, Assembly, Metagenomics | -megahit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit | -
- | megahit_contig2fastg | -1.1.3 | -1.2.9 | -megahit | -To update | -megahit | -MEGAHIT | -Genome assembly | -Metagenomics, Sequencing, Ecology, Sequence assembly | -A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) | -Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. | -- | To update | -https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp | -Sequence Analysis, Assembly, Metagenomics | -megahit_contig2fastg | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg | -
- | megan | -6.21.7 | -6.25.9 | -megan | -To update | -megan | -MEGAN | -Sequence analysis, Taxonomic classification | -Sequence analysis | -MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). | -Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzerÂť) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. | -- | To update | -https://github.com/husonlab/megan-ce | -Sequence Analysis | -megan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan | -
- | meme | -5.4.1 | -5.5.5 | -meme | -To update | -meme_fimo | -meme_fimo | -Sequence motif discovery, Nucleic acid feature detection, Protein feature detection, Statistical calculation | -Sequence analysis, Genetic variation, Statistics and probability, Data mining | -The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. | -A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. | -- | To update | -http://meme-suite.org/ | -ChIP-seq | -meme | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme | -
- | meme_chip | -4.11.2 | -1.3.26 | -graphicsmagick | -To update | -- | - | - | - | Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. | -- | - | To update | -http://meme-suite.org/ | -ChIP-seq | -meme_chip | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip | -
- | meningotype | -0.8.5 | -0.8.5 | -meningotype | -Up-to-date | -- | - | - | - | Assign sequence type to N. meningitidis genome assemblies | -- | - | Up-to-date | -https://github.com/MDU-PHL/meningotype | -Sequence Analysis | -meningotype | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype | -
- | merlin | -1.1.2 | -1.1.2 | -merlin | -Up-to-date | -merlin | -Merlin | -Haplotype mapping, Genetic mapping | -GWAS study, Mapping | -Pedigree Analysis package | -Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation | -- | Up-to-date | -http://csg.sph.umich.edu/abecasis/Merlin/ | -Variant Analysis | -merlin | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ | -
- | merqury | -1.3 | -1.3 | -merqury | -Up-to-date | -merqury | -Merqury | -Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly | -Sequence assembly, Whole genome sequencing, Plant biology | -Merqury is a tool for evaluating genomes assemblies based of k-mer operations. | -Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. | -- | Up-to-date | -https://github.com/marbl/merqury | -Assembly | -merqury | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury | -
- | meryl | -1.3 | -1.3 | -merqury | -Up-to-date | -meryl | -Meryl | -k-mer counting | -Whole genome sequencing, Genomics, Sequence analysis, Sequencing | -Meryl a k-mer counter. | -Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. | -- | Up-to-date | -https://github.com/marbl/meryl | -Assembly | -meryl | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl | -
- | metabat2 | -2.15 | -2.15 | -metabat2 | -Up-to-date | -MetaBAT_2 | -MetaBAT 2 | -Read binning, Sequence assembly, Genome annotation | -Metagenomics, Sequence assembly, Metagenomic sequencing | -MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. | -an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning | -- | Up-to-date | -https://bitbucket.org/berkeleylab/metabat/src/master/ | -Metagenomics | -metabat2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ | -
- | metaeuk | -5.34c21f2 | -6.a5d39d9 | -metaeuk | -To update | -MetaEuk | -MetaEuk | -Homology-based gene prediction | -Metagenomics, Gene and protein families | -MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. | -MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics | -- | To update | -https://github.com/soedinglab/metaeuk | -Sequence Analysis, Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk | -
- | metagenomeseq | -1.16.0-0.0.1 | -1.43.0 | -bioconductor-metagenomeseq | -To update | -metagenomeseq | -metagenomeSeq | -Sequence visualisation, Statistical calculation | -Metagenomics, Sequencing | -metagenomeSeq Normalization | -Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. | -- | To update | -- | Metagenomics | -metagenomeseq_normalization | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq | -
- | metaphlan | -4.0.6 | -4.1.0 | -metaphlan | -To update | -metaphlan | -MetaPhlAn | -Nucleic acid sequence analysis, Phylogenetic tree analysis | -Metagenomics, Phylogenomics | -MetaPhlAn for Metagenomic Phylogenetic Analysis | -Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. | -- | To update | -https://github.com/biobakery/MetaPhlAn | -Metagenomics | -metaphlan | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ | -
- | migmap | -1.0.3 | -1.0.3 | -migmap | -Up-to-date | -MiGMAP | -MiGMAP | -Sequence analysis, Read mapping | -Immunoproteins, genes and antigens, Sequence analysis | -mapper for full-length T- and B-cell repertoire sequencing | -Mapper for full-length T- and B-cell repertoire sequencing. | -- | Up-to-date | -https://github.com/mikessh/migmap | -RNA, Sequence Analysis | -migmap | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap | -
- | minia | -3.2.6 | -3.2.6 | -minia | -Up-to-date | -minia | -Minia | -Genome assembly | -Sequence assembly | -Short-read assembler based on a de Bruijn graph | -Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | -- | Up-to-date | -https://gatb.inria.fr/software/minia/ | -Assembly | -minia | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia | -
- | miniasm | -0.3_r179 | -0.3 | -miniasm | -To update | -- | - | - | - | Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) | -- | - | To update | -https://github.com/lh3/miniasm | -Assembly | -miniasm | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm | -
- | minimap2 | -2.26 | -2.26 | -minimap2 | -Up-to-date | -minimap2 | -Minimap2 | -Pairwise sequence alignment | -Mapping | -A fast pairwise aligner for genomic and spliced nucleotide sequences | -Pairwise aligner for genomic and spliced nucleotide sequences | -- | Up-to-date | -https://github.com/lh3/minimap2 | -Next Gen Mappers | -minimap2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 | -
- | miniprot | -0.12 | -0.12 | -miniprot | -Up-to-date | -- | - | - | - | Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. | -- | - | Up-to-date | -https://github.com/lh3/miniprot | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot | -
- | mirnature | -1.1 | -1.1 | -mirnature | -Up-to-date | -- | - | - | - | Computational detection of canonical microRNAs | -- | - | Up-to-date | -https://github.com/Bierinformatik/miRNAture | -RNA, Sequence Analysis | -mirnature | -iuc | -https://github.com/Bierinformatik/miRNAture | -
- | mitobim | -1.9.1 | -1.9.1 | -mitobim | -Up-to-date | -- | - | - | - | assemble mitochondrial genomes | -- | - | Up-to-date | -https://github.com/chrishah/MITObim | -Assembly | -mitobim | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim | -
- | mitos | -1.1.5 | -2.1.7 | -mitos | -To update | -mitos | -MITOS | -Genome annotation | -Zoology, Whole genome sequencing | -de-novo annotation of metazoan mitochondrial genomes | -De novo metazoan mitochondrial genome annotation. | -- | To update | -http://mitos.bioinf.uni-leipzig.de/ | -Sequence Analysis | -mitos | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos | -
- | mlst | -2.22.0 | -2.23.0 | -mlst | -To update | -mlst | -MLST | -Taxonomic classification | -Immunoproteins, genes and antigens | -Scan contig files against PubMLST typing schemes | -Multi Locus Sequence Typing from an assembled genome or from a set of reads. | -- | To update | -https://github.com/tseemann/mlst | -Sequence Analysis | -mlst | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst | -
- | moabs | -1.3.4.6 | -1.3.9.0 | -moabs | -To update | -- | - | - | - | MOABS for differential methylation analysis on Bisulfite sequencing data. | -- | - | To update | -https://github.com/sunnyisgalaxy/moabs | -Epigenetics | -moabs | -iuc | -https://github.com/sunnyisgalaxy/moabs | -
- | mosdepth | -0.3.6 | -0.3.6 | -mosdepth | -Up-to-date | -- | - | - | - | fast and flexible BAM/CRAM depth calculation | -- | - | Up-to-date | -https://github.com/brentp/mosdepth | -SAM | -mosdepth | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth | -
- | mothur | -1.0 | -1.48.0 | -mothur | -To update | -mothur | -mothur | -DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis | -Microbial ecology, Taxonomy, Sequence analysis, Phylogeny | -Mothur wrappers | -Open-source, platform-independent, community-supported software for describing and comparing microbial communities | -- | To update | -https://www.mothur.org | -Metagenomics | -mothur | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur | -
- | msaboot | -0.1.2 | -0.1.2 | -msaboot | -Up-to-date | -- | - | - | - | A multiple sequences alignment bootstrapping tool. | -- | - | Up-to-date | -https://github.com/phac-nml/msaboot | -Fasta Manipulation | -msaboot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot | -
- | multigps | -0.74.0 | -- | fonts-conda-ecosystem | -To update | -- | - | - | - | Analyzes collections of multi-condition ChIP-seq data. | -- | - | To update | -http://mahonylab.org/software/multigps/ | -ChIP-seq | -multigps | -iuc | -- |
- | multigsea | -1.12.0 | -1.12.0 | -bioconductor-multigsea | -Up-to-date | -multiGSEA | -multiGSEA | -Gene-set enrichment analysis, Aggregation, Pathway analysis | -Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules | -GSEA-based pathway enrichment analysis for multi-omics data | -A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. | -- | Up-to-date | -https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html | -Transcriptomics, Proteomics, Statistics | -multigsea | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea | -
- | multiqc | -1.11 | -1.21 | -multiqc | -To update | -multiqc | -MultiQC | -Validation | -Sequencing, Bioinformatics | -MultiQC aggregates results from bioinformatics analyses across many samples into a single report | -MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. | -- | To update | -http://multiqc.info/ | -Fastq Manipulation, Statistics, Visualization | -multiqc | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc | -
- | mummer4 | -4.0.0rc1 | -4.0.0rc1 | -mummer4 | -Up-to-date | -mumer4 | -MUMmer4 | -Multiple sequence alignment | -Sequence analysis, Human genetics | -Mummer4 Tools | -System for rapidly aligning large DNA sequences to one another. | -- | Up-to-date | -https://github.com/mummer4/mummer | -Sequence Analysis | -mummer4 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 | -
- | mykrobe | -0.10.0 | -0.13.0 | -mykrobe | -To update | -Mykrobe | -Mykrobe | -Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming | -Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics | -Antibiotic resistance predictions | -Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed | -- | To update | -https://github.com/Mykrobe-tools/mykrobe | -Sequence Analysis | -mykrobe | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe | -
- | mzmine | -3.9.0 | -3.9.0 | -mzmine | -Up-to-date | -mzmine | -MZmine | -Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation | -Proteomics, Metabolomics, Proteomics experiment, Small molecules | -mass-spectrometry data processing, with the main focus on LC-MS data | -Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. | -- | Up-to-date | -http://mzmine.github.io/ | -Metabolomics | -mzmine_batch | -iuc | -https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ | -
- | naltorfs | -0.1.2 | -0.1.2 | -naltorfs | -Up-to-date | -- | - | - | - | nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) | -- | - | Up-to-date | -https://github.com/BlankenbergLab/nAltORFs | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ | -
- | nanocompore | -1.0.0rc3.post2 | -1.0.4 | -nanocompore | -To update | -Nanocompore | -Nanocompore | -Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting | -Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites | -Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. | -RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro | -- | To update | -https://nanocompore.rna.rocks/ | -Sequence Analysis | -nanocompore | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore | -
- | nanoplot | -1.41.0 | -1.42.0 | -nanoplot | -To update | -- | - | - | - | Plotting tool for long read sequencing data and alignments | -- | - | To update | -https://github.com/wdecoster/NanoPlot | -Visualization | -nanoplot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ | -
- | nanopolishcomp | -0.6.11 | -0.6.12 | -nanopolishcomp | -To update | -- | - | - | - | NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. | -- | - | To update | -https://a-slide.github.io/NanopolishComp | -Sequence Analysis | -nanopolishcomp | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp | -
- | ncbi_acc_download | -0.2.8 | -0.2.8 | -ncbi-acc-download | -Up-to-date | -- | - | - | - | Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API | -- | - | Up-to-date | -https://github.com/kblin/ncbi-acc-download | -Data Source | -ncbi_acc_download | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download | -
- | ncbi_datasets | -15.19.1 | -- | ncbi-datasets-cli | -To update | -ncbi_datasets | -NCBI Datasets | -Data handling, Sequence database search, Data retrieval | -Biological databases | -NCBI datasets downloads biological sequence data across all domains of life from NCBI. | -NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. | -- | To update | -https://github.com/ncbi/datasets | -Data Source | -ncbi_datasets | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets | -
- | ncbi_entrez_direct | -16.2 | -16.2 | -entrez-direct | -Up-to-date | -- | - | - | - | NCBI Entrez Direct allow fetching data from NCBI Databases | -- | - | Up-to-date | -http://www.ncbi.nlm.nih.gov/books/NBK179288/ | -Data Source | -ncbi_entrez_direct | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct | -
- | ncbi_entrez_eutils | -1.70 | -- | python | -To update | -- | - | - | - | NCBI Entrez E-Utilties allow fetching data from NCBI Databases | -- | - | To update | -https://www.ncbi.nlm.nih.gov/books/NBK25501/ | -Data Source | -ncbi_entrez_eutils | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils | -
- | ncbi_fcs_gx | -0.5.0 | -0.5.0 | -ncbi-fcs-gx | -Up-to-date | -- | - | - | - | FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). | -- | - | Up-to-date | -https://github.com/ncbi/fcs-gx | -Sequence Analysis | -ncbi_fcs_gx | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx | -
- | necat | -0.0.1_update20200803 | -0.0.1_update20200803 | -necat | -Up-to-date | -necat | -NECAT | -De-novo assembly | -Sequence assembly | -Error correction and de-novo assembly for ONT Nanopore reads | -NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. | -- | Up-to-date | -https://github.com/xiaochuanle/NECAT | -Assembly | -necat | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat | -
- | newick_utils | -1.6+galaxy1 | -1.6 | -newick_utils | -To update | -newick_utilities | -Newick Utilities | -Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction | -Phylogeny, Genomics, Computer science | -Perform operations on Newick trees | -The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. | -- | To update | -http://cegg.unige.ch/newick_utils | -Visualization, Metagenomics | -newick_utils | -iuc | -https://github.com/tjunier/newick_utils | -
- | nextclade | -2.7.0 | -2.14.0 | -nextalign | -To update | -- | - | - | - | Identify differences between your sequences and a reference sequence used by Nextstrain | -- | - | To update | -https://github.com/nextstrain/nextclade | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade | -
- | ngmlr | -0.2.7 | -0.2.7 | -ngmlr | -Up-to-date | -ngmlr | -NGMLR | -DNA mapping, Sequence alignment, Genetic variation analysis | -Sequencing, Mapping, DNA structural variation | -CoNvex Gap-cost alignMents for Long Reads | -An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. | -- | Up-to-date | -https://github.com/philres/ngmlr | -Next Gen Mappers | -ngmlr | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr | -
- | ngsutils | -- | 0.5.9 | -ngsutils | -To update | -ngsutils | -NGSUtils | -Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering | -Genomics, Transcriptomics | -NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. | -NGSUtils is a suite of software tools for working with next-generation sequencing datasets | -- | To update | -https://github.com/ngsutils/ngsutils | -SAM | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils | -
- | nonpareil | -3.1.1 | -3.4.1 | -nonpareil | -To update | -- | - | - | - | Estimate average coverage in metagenomic datasets | -- | - | To update | -http://nonpareil.readthedocs.io | -Metagenomics | -nonpareil | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil | -
- | novoplasty | -4.3.1 | -4.3.5 | -novoplasty | -To update | -- | - | - | - | NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. | -- | - | To update | -https://github.com/ndierckx/NOVOPlasty | -Assembly | -novoplasty | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty | -
- | nugen_nudup | -2.3.3 | -2.3.3 | -nudup | -Up-to-date | -- | - | - | - | Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. | -- | - | Up-to-date | -http://nugentechnologies.github.io/nudup/ | -SAM, Metagenomics, Sequence Analysis, Transcriptomics | -nugen_nudup | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup | -
- | obitools | -1.2.13 | -1.2.13 | -obitools | -Up-to-date | -obitools | -OBITools | -Sequence analysis, Sequence analysis | -Sequence analysis, DNA, Sequencing | -OBITools is a set of programs developed to simplify the manipulation of sequence files | -Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. | -- | Up-to-date | -http://metabarcoding.org/obitools | -Sequence Analysis | -obitools | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools | -
- | ococo | -0.1.2.6 | -0.1.2.6 | -ococo | -Up-to-date | -- | - | - | - | Variant detection of SNVs | -- | - | Up-to-date | -https://github.com/karel-brinda/ococo | -Variant Analysis | -ococo | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo | -
- | odgi | -0.3 | -0.8.4 | -odgi | -To update | -- | - | - | - | Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. | -- | - | To update | -https://github.com/vgteam/odgi | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ | -
- | omark | -0.3.0 | -- | - | To update | -- | - | - | - | Proteome quality assessment software | -- | - | To update | -https://github.com/DessimozLab/OMArk | -Sequence Analysis | -omark | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ | -
- | ont_fast5_api | -3.1.3 | -4.1.3 | -ont-fast5-api | -To update | -- | - | - | - | ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. | -- | - | To update | -https://github.com/nanoporetech/ont_fast5_api/ | -Nanopore | -ont_fast5_api | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api | -
- | onto_toolkit | -1.45 | -1.45 | -perl-onto-perl | -Up-to-date | -- | - | - | - | ONTO-Toolkit is a collection of tools for managing ontologies. | -- | - | Up-to-date | -http://search.cpan.org/~easr/ONTO-PERL-1.45/ | -Ontology Manipulation | -onto_toolkit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit | -
- | optdoe | -v2.0.2 | -- | doebase | -To update | -- | - | - | - | Optimal Design Of Experiment | -- | - | To update | -https://github.com/pablocarb/doebase | -Synthetic Biology | -optdoe | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe | -
- | optitype | -1.3.5 | -1.3.5 | -optitype | -Up-to-date | -- | - | - | - | Precision HLA typing from NGS data | -- | - | Up-to-date | -https://github.com/FRED-2/OptiType | -Sequence Analysis | -optitype | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 | -
- | orfipy | -0.0.4 | -0.0.4 | -orfipy | -Up-to-date | -orfipy | -orfipy | -Coding region prediction, Database search, Transcriptome assembly, De-novo assembly | -Computer science, RNA-Seq, Transcriptomics, Small molecules | -Galaxy wrapper for ORFIPY | -A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. | -- | Up-to-date | -https://github.com/urmi-21/orfipy | -Sequence Analysis | -orfipy | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy | -
- | orthofinder | -2.5.5 | -2.5.5 | -orthofinder | -Up-to-date | -OrthoFinder | -OrthoFinder | -Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment | -Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis | -Accurate inference of orthologous gene groups made easy | -OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. | -- | Up-to-date | -https://github.com/davidemms/OrthoFinder | -Phylogenetics, Sequence Analysis | -orthofinder | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder | -
- | packaged_annotation_loader | -0.1 | -- | python | -To update | -- | - | - | - | Tool to make cached genome annotation data available as a list of datasets collection | -- | - | To update | -- | Data Source | -packaged_annotation_loader | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader | -
- | pangolin | -4.3 | -4.3 | -pangolin | -Up-to-date | -- | - | - | - | Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. | -- | - | Up-to-date | -https://github.com/cov-lineages/pangolin | -Sequence Analysis | -pangolin | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin | -
- | parse_mito_blast | -1.0.2 | -1.0.2 | -parse_mito_blast | -Up-to-date | -- | - | - | - | Filtering blast out from querying assembly against mitochondrial database. | -- | - | Up-to-date | -https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py | -Sequence Analysis | -parse_mito_blast | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast | -
- | pathview | -1.34.0 | -1.42.0 | -bioconductor-pathview | -To update | -pathview | -pathview | -Pathway or network analysis, Pathway or network visualisation | -Molecular interactions, pathways and networks, Systems biology, Data visualisation | -Pathview is a tool set for pathway based data integration and visualization. | -Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. | -- | To update | -https://bioconductor.org/packages/release/bioc/html/pathview.html | -Statistics, RNA, Micro-array Analysis | -pathview | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview | -
- | pbgcpp | -2.0.2 | -2.0.2 | -pbgcpp | -Up-to-date | -genomicconsensus | -GenomicConsensus | -Variant calling | -Mapping | -Compute genomic consensus and call variants using PacBio reads mapped to a reference | -The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. | -- | Up-to-date | -https://github.com/PacificBiosciences/gcpp | -Variant Analysis | -pbgcpp | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp | -
- | pbmm2 | -1.13.1 | -1.13.1 | -pbmm2 | -Up-to-date | -pbmm2 | -pbmm2 | -Pairwise sequence alignment, Sorting | -Mapping | -A minimap2 SMRT wrapper for PacBio data. | -pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. | -- | Up-to-date | -https://github.com/PacificBiosciences/pbmm2 | -Next Gen Mappers | -pbmm2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 | -
- | pe_histogram | -1.0.1 | -- | openjdk | -To update | -- | - | - | - | Contains a tool that produces an insert size histogram for a paired-end BAM file. | -- | - | To update | -https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram | -Graphics | -pe_histogram | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram | -
- | peakzilla | -1.0 | -- | python | -To update | -- | - | - | - | Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. | -- | - | To update | -https://github.com/steinmann/peakzilla | -ChIP-seq | -peakzilla | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla | -
- | pear | -0.9.6 | -0.9.6 | -pear | -Up-to-date | -pear | -PEAR | -Sequence merging | -Sequence assembly | -PEAR evaluates all possible paired-end read overlaps | -Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. | -- | Up-to-date | -- | - | pear | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear | -
- | pharokka | -1.3.2 | -- | \n pharokka\n | -To update | -\n pharokka\n | -- | - | - | rapid standardised annotation tool for bacteriophage genomes and metagenomes | -- | - | To update | -https://github.com/gbouras13/pharokka | -Genome annotation | -pharokka | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka | -
- | phyloseq | -1.38.0 | -1.46.0 | -bioconductor-phyloseq | -To update | -phyloseq | -phyloseq | -Deposition, Analysis, Visualisation | -Microbiology, Sequence analysis, Metagenomics | -Handling and analysis of high-throughput microbiome census data | -Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. | -- | To update | -https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html | -Metagenomics | -phyloseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq | -
- | phyml | -3.3.20220408 | -3.3.20220408 | -phyml | -Up-to-date | -phyml | -PhyML | -Phylogenetic tree generation (maximum likelihood and Bayesian methods) | -Phylogenetics, Bioinformatics, Phylogenetics | -PhyML is a phylogeny software based on the maximum-likelihood principle. | -Phylogenetic estimation software using Maximum Likelihood | -- | Up-to-date | -http://www.atgc-montpellier.fr/phyml/ | -Phylogenetics | -phyml | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml | -
- | picard | -3.1.1 | -3.1.1 | -picard | -Up-to-date | -picard_fastqtosam | -picard_fastqtosam | -Formatting | -Sequencing | -Picard SAM/BAM manipulation tools. | -Create an unaligned BAM file. | -- | Up-to-date | -http://broadinstitute.github.io/picard/ | -SAM | -picard | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard | -
- | pick_value | -0.2.0 | -- | - | To update | -- | - | - | - | Compose a text parameter value using text, integer and float values | -- | - | To update | -- | Text Manipulation | -pick_value | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value | -
- | picrust | -1.1.1 | -1.1.4 | -picrust | -To update | -picrust | -PICRUSt | -Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding | -Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing | -PICRUSt wrappers | -PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. | -- | To update | -https://picrust.github.io/picrust/ | -Metagenomics | -picrust | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust | -
- | picrust2 | -2.5.1 | -2.5.2 | -picrust2 | -To update | -picrust2 | -PICRUSt2 | -Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis | -Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing | -PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States | -PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. | -- | To update | -https://github.com/picrust/picrust2/wiki | -Metagenomics | -picrust2 | -iuc | -https://github.com/picrust/picrust2 | -
- | pilon | -1.20.1 | -1.24 | -pilon | -To update | -pilon | -pilon | -Sequence assembly, Analysis, Read alignment | -Assembly | -pilon is a tool for assembly improvement and variant analysis in bacteria | -Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. | -- | To update | -- | Variant Analysis | -pilon | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon | -
- | pipelign | -0.2 | -0.2 | -pipelign | -Up-to-date | -- | - | - | - | Multipe sequence alignment | -- | - | Up-to-date | -https://github.com/asmmhossain/pipelign/ | -Next Gen Mappers | -pipelign | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign | -
- | pizzly | -0.37.3.1 | -0.37.3 | -pizzly | -To update | -- | - | - | - | Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. | -- | - | To update | -https://github.com/pmelsted/pizzly/ | -Transcriptomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ | -
- | plasflow | -1.1.0 | -1.1.0 | -plasflow | -Up-to-date | -- | - | - | - | PlasFlow - Prediction of plasmid sequences in metagenomic contigs. | -- | - | Up-to-date | -https://github.com/smaegol/PlasFlow | -Sequence Analysis | -plasflow | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow | -
- | plasmidfinder | -2.1.6 | -2.1.6 | -plasmidfinder | -Up-to-date | -PlasmidFinder | -PlasmidFinder | -Genome assembly, Scaffolding, Multilocus sequence typing | -Whole genome sequencing, Sequence assembly, Mapping, Probes and primers | -"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" | -PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). | -- | Up-to-date | -https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ | -Sequence Analysis | -plasmidfinder | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder | -
- | plink | -1.90b6.21 | -1.90b6.21 | -plink | -Up-to-date | -plink | -PLINK | -Genetic variation analysis | -GWAS study | -PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. | -Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. | -- | Up-to-date | -https://www.cog-genomics.org/plink | -Genome-Wide Association Study | -plink | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink | -
- | polypolish | -0.5.0 | -0.6.0 | -polypolish | -To update | -Polypolish | -Polypolish | -Genome assembly, Read mapping, Mapping assembly, Sequencing error detection | -Sequence assembly, Sequence composition, complexity and repeats, Mapping | -"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." | -Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. | -- | To update | -https://github.com/rrwick/Polypolish | -Sequence Analysis | -polypolish | -iuc | -https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish | -
- | porechop | -- | 0.2.4 | -porechop | -To update | -- | - | - | - | Porechop - Finding and removing adapters from Oxford Nanopore reads | -- | - | To update | -https://github.com/rrwick/Porechop | -Fasta Manipulation, Fastq Manipulation | -porechop | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop | -
- | poretools | -0.6.1a1 | -0.6.1a1 | -poretools | -Up-to-date | -poretools | -Poretools | -Nucleic acid sequence analysis | -DNA, Sequencing | -A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. | -Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. | -- | Up-to-date | -https://poretools.readthedocs.io/en/latest/ | -Fasta Manipulation, Fastq Manipulation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools | -
- | presto | -0.6.2 | -0.7.2 | -presto | -To update | -presto | -pRESTO | -Nucleic acid sequence analysis | -Sequencing, DNA, Immunology | -pRESTO toolkit for immune repertoire analysis. | -Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. | -- | To update | -https://presto.readthedocs.io/ | -Sequence Analysis | -presto | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto | -
- | pretext | -0.0.6 | -0.0.6 | -pretextgraph | -Up-to-date | -- | - | - | - | Process genome contacts maps processing images. | -- | - | Up-to-date | -https://github.com/wtsi-hpag/PretextSnapshot | -Sequence Analysis | -suite_pretext | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext | -
- | prinseq | -@TOOL_VERSION+galaxy2 | -0.20.4 | -prinseq | -To update | -prinseq | -PRINSEQ | -Read pre-processing, Sequence trimming, Sequence contamination filtering | -Transcriptomics, Metagenomics, Genomics | -PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets | -PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. | -- | To update | -http://prinseq.sourceforge.net/manual.html | -Fastq Manipulation, Metagenomics | -prinseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ | -
- | progressivemauve | -- | snapshot_2015_02_13 | -progressivemauve | -To update | -- | - | - | - | Mauve/ProgressiveMauve Multiple Sequence Aligner | -- | - | To update | -- | Sequence Analysis | -progressivemauve | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve | -
- | prokka | -1.14.6 | -1.14.6 | -prokka | -Up-to-date | -prokka | -Prokka | -Gene prediction, Coding region prediction, Genome annotation | -Genomics, Model organisms, Virology | -Rapid annotation of prokaryotic genomes | -Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. | -- | Up-to-date | -http://github.com/tseemann/prokka | -Sequence Analysis | -prokka | -crs4 | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ | -
- | prot-scriber | -0.1.4 | -0.1.5 | -prot-scriber | -To update | -- | - | - | - | Protein annotation of short human readable descriptions | -- | - | To update | -https://github.com/usadellab/prot-scriber | -Proteomics | -prot_scriber | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber | -
- | proteinortho | -6.3.1 | -6.3.1 | -proteinortho | -Up-to-date | -proteinortho | -Proteinortho | -Homology-based gene prediction | -Phylogeny | -Proteinortho is a tool to detect orthologous proteins/genes within different species. | -Proteinortho is a tool to detect orthologous genes within different species | -- | Up-to-date | -https://gitlab.com/paulklemm_PHD/proteinortho | -Proteomics | -proteinortho | -iuc | -https://gitlab.com/paulklemm_PHD/proteinortho | -
- | psiclass | -1.0.3 | -1.0.3 | -psiclass | -Up-to-date | -psiclass | -- | - | - | PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. | -- | - | Up-to-date | -https://github.com/splicebox/PsiCLASS | -Transcriptomics | -psiclass | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass | -
- | pureclip | -1.0.4 | -1.3.1 | -pureclip | -To update | -- | - | - | - | PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data | -- | - | To update | -https://github.com/skrakau/PureCLIP | -Sequence Analysis, RNA, CLIP-seq | -pureclip | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip | -
- | purge_dups | -1.2.6 | -1.2.6 | -purge_dups | -Up-to-date | -purge_dups | -purge_dups | -Genome assembly, Read binning, Scaffolding | -Sequence assembly | -Purge haplotigs and overlaps in an assembly based on read depth | -Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences | -- | Up-to-date | -https://github.com/dfguan/purge_dups | -Assembly | -purge_dups | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups | -
- | pycoqc | -2.5.2 | -2.5.2 | -pycoqc | -Up-to-date | -- | - | - | - | QC metrics for ONT Basecalling | -- | - | Up-to-date | -https://github.com/tleonardi/pycoQC | -Nanopore | -pycoqc | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc | -
- | pyega3 | -5.0.2 | -5.1.0 | -pyega3 | -To update | -- | - | - | - | EGA python client uses the EGA REST API to download authorized datasets and files. | -- | - | To update | -https://github.com/EGA-archive/ega-download-client | -Data Source | -ega_download_client | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 | -
- | pygenometracks | -3.8 | -3.8 | -pygenometracks | -Up-to-date | -- | - | - | - | pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. | -- | - | Up-to-date | -https://github.com/deeptools/pyGenomeTracks | -Visualization | -pygenometracks | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks | -
- | pysradb | -1.4.2 | -2.2.0 | -pysradb | -To update | -pysradb | -pysradb | -Deposition, Data retrieval | -Sequencing, Gene transcripts, Bioinformatics | -pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. | -Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. | -- | To update | -https://github.com/saketkc/pysradb | -Sequence Analysis | -pysradb_search | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb | -
- | qfilt | -1.0.0+galaxy1 | -0.0.1 | -qfilt | -To update | -- | - | - | - | Filter sequencing data | -- | - | To update | -https://github.com/veg/qfilt | -Fastq Manipulation | -qfilt | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt | -
- | qiime_add_on | -- | 1.9.1 | -qiime | -To update | -- | - | - | - | QIIME to perform microbial community analysis | -- | - | To update | -http://www.qiime.org | -Metagenomics | -qiime | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ | -
- | qiime_core | -- | 1.9.1 | -qiime | -To update | -- | - | - | - | QIIME to perform microbial community analysis | -- | - | To update | -http://www.qiime.org | -Metagenomics | -qiime | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ | -
- | qq_tools | -0.1.0 | -0.1.4 | -r-qqman | -To update | -- | - | - | - | - | - | - | To update | -https://CRAN.R-project.org/package=qqman | -Visualization, Variant Analysis | -- | iuc | -- |
- | qualimap | -2.2.2d | -2.3 | -qualimap | -To update | -qualimap | -QualiMap | -Sequencing quality control | -Data quality management | -- | Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. | -- | To update | -http://qualimap.bioinfo.cipf.es/ | -Sequence Analysis, Transcriptomics, SAM | -qualimap | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap | -
- | quast | -5.2.0 | -5.2.0 | -quast | -Up-to-date | -quast | -QUAST | -Visualisation, Sequence assembly validation | -Sequence assembly | -Quast (Quality ASsessment Tool) evaluates genome assemblies. | -QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. | -- | Up-to-date | -http://quast.bioinf.spbau.ru/ | -Assembly | -quast | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast | -
- | query_impc | -0.9.0 | -- | requests | -To update | -- | - | - | - | Contains a tool to query the IMPC database. | -- | - | To update | -https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc | -Convert Formats, Web Services | -query_impc | -iuc | -https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc | -
- | query_tabular | -3.3.0 | -- | python | -To update | -- | - | - | - | Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output | -- | - | To update | -- | Text Manipulation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular | -
- | quickmerge | -0.3 | -0.3 | -quickmerge | -Up-to-date | -quickmerge | -quickmerge | -Genome assembly, Scaffolding, De-novo assembly, Genotyping | -Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype | -Merge long-read and hybrid assemblies to increase contiguity | -Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. | -- | Up-to-date | -https://github.com/mahulchak/quickmerge | -Assembly | -quickmerge | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge | -
- | raceid | -0.2.3 | -0.1.3 | -r-raceid | -To update | -- | - | - | - | RaceID3, StemID2, FateID - scRNA analysis | -- | - | To update | -https://github.com/dgrun/RaceID3_StemID2_package/ | -Transcriptomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 | -
- | ragtag | -2.1.0 | -2.1.0 | -ragtag | -Up-to-date | -ragtag | -ragtag | -Genome assembly | -Sequence assembly | -Reference-guided scaffolding of draft genomes tool. | -RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. | -- | Up-to-date | -https://github.com/malonge/RagTag | -Assembly | -ragtag | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag | -
- | rapidnj | -2.3.2 | -2.3.2 | -rapidnj | -Up-to-date | -rapidnj | -RapidNJ | -Phylogenetic tree generation | -Phylogeny | -Galaxy wrapper for the RapidNJ tool | -A tool for fast canonical neighbor-joining tree construction. | -- | Up-to-date | -https://birc.au.dk/software/rapidnj/ | -Phylogenetics | -rapidnj | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj | -
- | rasusa | -0.8.0 | -0.8.0 | -rasusa | -Up-to-date | -rasusa | -rasusa | -- | - | Randomly subsample sequencing reads to a specified coverage | -Produces an unbiased subsample of your reads | -- | Up-to-date | -https://github.com/mbhall88/rasusa | -Sequence Analysis | -rasusa | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa | -
- | raven | -1.8.0 | -1.8.3 | -raven-assembler | -To update | -- | - | - | - | Raven is a de novo genome assembler for long uncorrected reads. | -- | - | To update | -https://github.com/lbcb-sci/raven | -Assembly | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven | -
- | raxml | -8.2.12 | -8.2.13 | -raxml | -To update | -raxml | -RAxML | -Sequence analysis, Phylogenetic tree analysis | -Phylogenetics, Sequence analysis | -RAxML - A Maximum Likelihood based phylogenetic inference | -A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. | -- | To update | -http://www.exelixis-lab.org/web/software/raxml/ | -Phylogenetics | -raxml | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml | -
- | rcorrector | -1.0.3+galaxy1 | -1.0.6 | -rcorrector | -To update | -rcorrector | -Rcorrector | -Sequencing error detection | -RNA, RNA-Seq, Sequencing | -Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. | -This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. | -- | To update | -https://github.com/mourisl/Rcorrector | -Fastq Manipulation | -rcorrector | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector | -
- | read_it_and_keep | -0.2.2 | -0.3.0 | -read-it-and-keep | -To update | -- | - | - | - | Rapid decontamination of SARS-CoV-2 sequencing reads | -- | - | To update | -https://github.com/GenomePathogenAnalysisService/read-it-and-keep | -Sequence Analysis | -read_it_and_keep | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep | -
- | recentrifuge | -1.14.0 | -1.14.0 | -recentrifuge | -Up-to-date | -Recentrifuge | -Recentrifuge | -Taxonomic classification, Expression analysis, Cross-assembly | -Metagenomics, Microbial ecology, Metagenomic sequencing | -"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." | -Robust comparative analysis and contamination removal for metagenomics. | -- | Up-to-date | -https://github.com/khyox/recentrifuge | -Metagenomics | -recentrifuge | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge | -
- | red | -2018.09.10 | -2018.09.10 | -red | -Up-to-date | -- | - | - | - | Red (REpeat Detector) | -- | - | Up-to-date | -https://github.com/BioinformaticsToolsmith/Red | -Sequence Analysis | -red | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/red | -
- | repeatmasker | -4.1.5 | -4.1.5 | -repeatmasker | -Up-to-date | -repeatmasker | -RepeatMasker | -Genome annotation | -Sequence analysis, Sequence composition, complexity and repeats | -RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | -A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). | -- | Up-to-date | -http://www.repeatmasker.org/ | -Sequence Analysis | -repeat_masker | -bgruening | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker | -
- | repeatmodeler | -2.0.5 | -- | - | To update | -- | - | - | - | RepeatModeler - Model repetitive DNA | -- | - | To update | -https://www.repeatmasker.org/RepeatModeler/ | -Genome annotation | -repeatmodeler | -csbl | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler | -
- | repmatch_gff3 | -- | - | matplotlib | -To update | -- | - | - | - | Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. | -- | - | To update | -- | ChIP-seq | -repmatch_gff3 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 | -
- | reshape2 | -1.4.2 | -- | r-reshape2 | -To update | -- | - | - | - | Flexibly restructure and aggregate data using just the two functions melt and dcast | -- | - | To update | -https://cran.r-project.org/web/packages/reshape2/index.html | -Text Manipulation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 | -
- | resize_coordinate_window | -1.0.2 | -- | python | -To update | -- | - | - | - | Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. | -- | - | To update | -- | Genomic Interval Operations | -resize_coordinate_window | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window | -
- | rgcca | -3.0.2 | -3.0.3 | -rgccacmd | -To update | -- | - | - | - | multi-block analysis | -- | - | To update | -https://github.com/rgcca-factory/RGCCA | -Statistics | -rgcca | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca | -
- | rgrnastar | -2.7.11a | -2.7.11b | -star | -To update | -star | -STAR | -Sequence alignment | -RNA-Seq, Transcriptomics | -RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper | -Ultrafast universal RNA-seq data aligner | -- | To update | -https://github.com/alexdobin/STAR | -Next Gen Mappers, Transcriptomics | -rgrnastar | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar | -
- | ribowaltz | -1.2.0 | -2.0 | -ribowaltz | -To update | -riboWaltz | -riboWaltz | -- | Computational biology | -Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data | -riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. | -- | To update | -https://github.com/LabTranslationalArchitectomics/riboWaltz | -Transcriptomics, RNA | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz | -
- | rnaquast | -2.2.3 | -2.2.3 | -rnaquast | -Up-to-date | -rnaQUAST | -rnaQUAST | -De-novo assembly, Transcriptome assembly, Sequence assembly validation | -Sequence assembly, Transcriptomics, RNA-seq | -rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. | -Quality assessment tool for de novo transcriptome assemblies. | -- | Up-to-date | -https://github.com/ablab/rnaquast | -Assembly, RNA | -rnaquast | -iuc | -https://git.ufz.de/lehmanju/rnaquast | -
- | roary | -3.13.0 | -3.13.0 | -roary | -Up-to-date | -roary | -Roary | -Genome assembly | -DNA, Genomics, Mapping | -Roary the pangenome pipeline | -A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. | -- | Up-to-date | -https://sanger-pathogens.github.io/Roary/ | -Sequence Analysis | -roary | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary | -
- | rp2biosensor | -3.2.1 | -- | rp2biosensor | -To update | -- | - | - | - | Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output | -- | - | To update | -https://github.com/brsynth/rp2biosensor | -Synthetic Biology | -rp2biosensor | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor | -
- | rp2paths | -1.5.1 | -- | rp2paths | -To update | -- | - | - | - | Enumerate and seperate the different pathways generated by RetroPath2.0 | -- | - | To update | -https://github.com/brsynth/rp2paths | -Synthetic Biology | -rp2paths | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths | -
- | rpbasicdesign | -1.2.2 | -- | rpbasicdesign | -To update | -- | - | - | - | Extracting enzyme IDs from rpSBML files | -- | - | To update | -https://github.com/brsynth/rpbasicdesign | -Synthetic Biology | -rpbasicdesign | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign | -
- | rpfba | -5.12.3 | -- | rptools | -To update | -- | - | - | - | Perform FBA for the RetroPath2.0 heterologous pathways | -- | - | To update | -https://github.com/brsynth/rptools/releases | -Synthetic Biology | -rpfba | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba | -
- | rptools | -5.13.1 | -- | rptools | -To update | -- | - | - | - | Suite of tools that work on rpSBML format | -- | - | To update | -https://github.com/brsynth/rptools | -Synthetic Biology | -rptools | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools | -
- | rrparser | -2.5.2 | -- | rrparser | -To update | -- | - | - | - | Reaction Rules Parser | -- | - | To update | -https://github.com/brsynth/RRParser | -Synthetic Biology | -rrparser | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser | -
- | rseqc | -5.0.1 | -5.0.3 | -rseqc | -To update | -rseqc | -RSeQC | -Data handling | -Sequencing | -an RNA-seq quality control package | -Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. | -- | To update | -https://code.google.com/p/rseqc/ | -Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization | -rseqc | -nilesh | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc | -
- | ruvseq | -1.26.0 | -1.36.0 | -bioconductor-ruvseq | -To update | -ruvseq | -RUVSeq | -Differential gene expression analysis | -Gene expression, RNA-seq | -Remove Unwanted Variation from RNA-Seq Data | -This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. | -- | To update | -https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html | -Transcriptomics, RNA, Statistics | -ruvseq | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq | -
- | salsa2 | -2.3 | -2.3 | -salsa2 | -Up-to-date | -SALSA | -SALSA | -Genome assembly, De-novo assembly, Scaffolding | -Sequence assembly, DNA binding sites, Mapping | -A tool to scaffold long read assemblies with Hi-C | -> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch | -- | Up-to-date | -https://github.com/marbl/SALSA | -Assembly | -salsa | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 | -
- | samblaster | -0.1.24 | -0.1.26 | -samblaster | -To update | -samblaster | -SAMBLASTER | -Split read mapping | -DNA, Sequencing, Mapping | -samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files | -A tool to mark duplicates and extract discordant and split reads from SAM files. | -- | To update | -https://github.com/GregoryFaust/samblaster | -SAM, Fastq Manipulation, Variant Analysis | -samblaster | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster | -
- | sansa | -0.0.8 | -0.1.1 | -sansa | -To update | -- | - | - | - | Sansa is a tool for structural variant annotation. | -- | - | To update | -https://github.com/dellytools/sansa | -Variant Analysis | -sansa | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa | -
- | sarscov2formatter | -1.0 | -1.0 | -sarscov2formatter | -Up-to-date | -- | - | - | - | sarscov2formatter custom script | -- | - | Up-to-date | -https://github.com/nickeener/sarscov2formatter | -Sequence Analysis | -sarscov2formatter | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter | -
- | sarscov2summary | -0.1 | -0.5 | -sarscov2summary | -To update | -- | - | - | - | sarscov2summary custom script | -- | - | To update | -https://github.com/nickeener/sarscov2summary | -Sequence Analysis | -sarscov2summary | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary | -
- | sbml2sbol | -0.1.13 | -- | sbml2sbol | -To update | -- | - | - | - | Convert SBML to SBOL format | -- | - | To update | -https://github.com/neilswainston/SbmlToSbol | -Synthetic Biology | -sbml2sbol | -iuc | -- |
- | scanpy | -1.9.6 | -1.7.2 | -scanpy | -To update | -scanpy | -SCANPY | -Differential gene expression analysis | -Gene expression, Cell biology, Genetics | -Scanpy – Single-Cell Analysis in Python | -Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. | -- | To update | -https://scanpy.readthedocs.io | -Transcriptomics, Sequence Analysis | -scanpy | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ | -
- | scater | -1.22.0 | -1.30.1 | -bioconductor-scater | -To update | -scater | -scater | -Read pre-processing, Sequencing quality control, Sequence visualisation | -RNA-seq, Quality affairs, Molecular genetics | -Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. | -Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. | -- | To update | -http://bioconductor.org/packages/scater/ | -Transcriptomics, RNA, Visualization | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater | -
- | sceasy | -0.0.7 | -0.0.7 | -r-sceasy | -Up-to-date | -- | - | - | - | Converter between difference single-cell formats | -- | - | Up-to-date | -https://github.com/cellgeni/sceasy/ | -Transcriptomics | -sceasy_convert | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ | -
- | schicexplorer | -4 | -7 | -schicexplorer | -To update | -- | - | - | - | scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. | -- | - | To update | -https://github.com/joachimwolff/schicexplorer | -Sequence Analysis, Transcriptomics, Visualization | -schicexplorer | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer | -
- | scikit-bio | -0.4.2 | -0.4.2 | -scikit-bio | -Up-to-date | -- | - | - | - | scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics | -- | - | Up-to-date | -http://scikit-bio.org/ | -Sequence Analysis | -scikit_bio | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio | -
- | scoary | -1.6.16 | -1.6.16 | -scoary | -Up-to-date | -- | - | - | - | Scoary calculates the assocations between all genes in the accessory genome and the traits. | -- | - | Up-to-date | -https://github.com/AdmiralenOla/Scoary | -Metagenomics | -scoary | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary | -
- | scpipe | -1.0.0+galaxy2 | -2.2.0 | -bioconductor-scpipe | -To update | -scpipe | -scPipe | -Genome annotation, Validation, Alignment, Visualisation | -Gene expression, RNA-seq, Sequencing | -A flexible preprocessing pipeline for single-cell RNA-sequencing data | -A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. | -- | To update | -http://bioconductor.org/packages/release/bioc/html/scPipe.html | -Transcriptomics, RNA, Statistics | -scpipe | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe | -
- | seacr | -1.3 | -1.3 | -seacr | -Up-to-date | -- | - | - | - | SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. | -- | - | Up-to-date | -https://github.com/FredHutch/SEACR | -Epigenetics, ChIP-seq | -seacr | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr | -
- | selenzy_wrapper | -0.3.0 | -0.3.0 | -selenzy_wrapper | -Up-to-date | -- | - | - | - | Performs enzyme selection from a reaction query. | -- | - | Up-to-date | -https://github.com/brsynth/selenzy-wrapper | -Synthetic Biology | -selenzy_wrapper | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper | -
- | semibin | -2.0.2 | -2.0.2 | -semibin | -Up-to-date | -semibin | -SemiBin | -Sequence assembly, Read binning | -Metagenomics, Machine learning, Microbial ecology, Sequence assembly | -SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks | -Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. | -- | Up-to-date | -https://semibin.readthedocs.io/en/latest/ | -Metagenomics | -semibin | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin | -
- | seq2hla | -2.3 | -2.3 | -seq2hla | -Up-to-date | -seq2hla | -Seq2HLA | -Read mapping, Genetic variation analysis | -Transcriptomics, Mapping | -Precision HLA typing and expression from RNAseq data | -seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. | -- | Up-to-date | -https://github.com/TRON-Bioinformatics/seq2HLA | -Sequence Analysis | -seq2hla | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla | -
- | seqcomplexity | -0.1.2 | -0.1.2 | -seqcomplexity | -Up-to-date | -- | - | - | - | Sequence complexity for raw reads | -- | - | Up-to-date | -https://github.com/stevenweaver/seqcomplexity | -Sequence Analysis | -- | iuc | -https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ | -
- | seqkit | -2.3.1 | -2.7.0 | -seqkit | -To update | -seqkit | -seqkit | -DNA transcription, Sequence trimming, DNA translation, Sequence conversion | -Database management, Sequence analysis | -A cross-platform and ultrafast toolkit for FASTA/Q file manipulation | -FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. | -- | To update | -https://bioinf.shenwei.me/seqkit/ | -Sequence Analysis | -seqkit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit | -
- | seqprep | -1.3.2 | -1.3.2 | -seqprep | -Up-to-date | -seqprep | -SeqPrep | -Nucleic acid design | -Genomics, Sequence assembly, Sequencing, Probes and primers | -Tool for merging paired-end Illumina reads and trimming adapters. | -Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. | -- | Up-to-date | -https://github.com/jstjohn/SeqPrep | -Fastq Manipulation, Sequence Analysis | -seqprep | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep | -
- | seqsero2 | -1.2.1 | -1.2.1 | -seqsero2 | -Up-to-date | -- | - | - | - | Salmonella serotype prediction from genome sequencing data | -- | - | Up-to-date | -https://github.com/denglab/SeqSero2 | -Sequence Analysis | -seqsero2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 | -
- | seqtk | -1.4 | -1.4 | -seqtk | -Up-to-date | -seqtk | -seqtk | -Data handling, Sequence file editing | -Data management | -Toolkit for processing sequences in FASTA/Q formats | -A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. | -- | Up-to-date | -https://github.com/lh3/seqtk | -Sequence Analysis | -seqtk | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk | -
- | seqwish | -0.7.5 | -0.7.9 | -seqwish | -To update | -- | - | - | - | Alignment to variation graph inducer | -- | - | To update | -https://github.com/ekg/seqwish | -Sequence Analysis, Variant Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ | -
- | seurat | -4.3.0.1 | -3.0.2 | -r-seurat | -To update | -- | - | - | - | A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data | -- | - | To update | -https://github.com/satijalab/seurat | -Transcriptomics, RNA, Statistics | -seurat | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat | -
- | shasta | -0.6.0 | -0.11.1 | -shasta | -To update | -- | - | - | - | Fast de novo assembly of long read sequencing data | -- | - | To update | -https://github.com/chanzuckerberg/shasta | -Assembly, Nanopore | -shasta | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta | -
- | shorah | -1.1.3 | -1.99.2 | -shorah | -To update | -shorah | -ShoRAH | -Haplotype mapping, Variant calling | -Metagenomics, Sequencing, Genetics | -Reconstruct haplotypes using ShoRAH in amplicon mode | -Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. | -- | To update | -https://github.com/cbg-ethz/shorah/blob/master/README.md | -Sequence Analysis | -shorah_amplicon | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah | -
- | shovill | -1.1.0 | -1.1.0 | -shovill | -Up-to-date | -shovill | -shovill | -Genome assembly | -Genomics, Microbiology, Sequence assembly | -Faster de novo assembly pipeline based around Spades | -Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. | -- | Up-to-date | -https://github.com/tseemann/shovill | -Assembly | -shovill | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill | -
- | sickle | -1.33.2 | -1.33 | -sickle-trim | -To update | -sickle | -sickle | -Sequence trimming | -Data quality management | -A windowed adaptive trimming tool for FASTQ files using quality | -A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. | -- | To update | -https://github.com/najoshi/sickle | -Fastq Manipulation, Sequence Analysis | -sickle | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle | -
- | simtext | -0.0.2 | -1.0.1 | -r-argparse | -To update | -- | - | - | - | A text mining framework for interactive analysis and visualization of similarities among biomedical entities. | -- | - | To update | -https://github.com/dlal-group/simtext | -Text Manipulation | -simtext | -iuc | -https://github.com/galaxyproject/tools-iuc/tools/simtext | -
- | sina | -1.7.2 | -1.7.2 | -sina | -Up-to-date | -sina | -SINA | -Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment | -Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy | -SINA reference based multiple sequence alignment | -Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment | -- | Up-to-date | -https://sina.readthedocs.io/en/latest/ | -Sequence Analysis | -sina | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina | -
- | sinto | -0.9.0 | -0.10.0 | -sinto | -To update | -- | - | - | - | Sinto single-cell analysis tools | -- | - | To update | -https://github.com/timoast/sinto | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto | -
- | slamdunk | -0.4.3 | -0.4.3 | -slamdunk | -Up-to-date | -- | - | - | - | Slamdunk maps and quantifies SLAMseq reads | -- | - | Up-to-date | -http://t-neumann.github.io/slamdunk | -RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers | -slamdunk | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk | -
- | sleuth | -0.30.1 | -0.30.1 | -r-sleuth | -Up-to-date | -sleuth | -sleuth | -Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation | -RNA-seq, Gene expression, Statistics and probability | -Sleuth is a program for differential analysis of RNA-Seq data. | -A statistical model and software application for RNA-seq differential expression analysis. | -- | Up-to-date | -https://github.com/pachterlab/sleuth | -Transcriptomics, RNA, Statistics | -sleuth | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth | -
- | smallgenomeutilities | -0.4.0 | -0.4.0 | -smallgenomeutilities | -Up-to-date | -v-pipe | -V-pipe | -Read pre-processing, Sequence alignment, Genetic variation analysis | -Genomics, Population genetics, Workflows, Virology, Sequencing | -Set of utilities for manipulating small viral genome data. | -Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. | -- | Up-to-date | -https://github.com/cbg-ethz/smallgenomeutilities | -Sequence Analysis | -smallgenomeutilities | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities | -
- | smudgeplot | -0.2.5 | -0.2.5 | -smudgeplot | -Up-to-date | -smudgeplots | -Smudgeplots | -Sequence trimming, Genotyping, k-mer counting | -Sequence assembly, Genetic variation, Mathematics | -Inference of ploidy and heterozygosity structure using whole genome sequencing | -Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 | -- | Up-to-date | -https://github.com/KamilSJaron/smudgeplot | -Assembly | -smudgeplot | -galaxy-australia | -https://github.com/galaxyproject/tools-iuc | -
- | snap | -2013_11_29 | -2013_11_29 | -snap | -Up-to-date | -snap | -SNAP | -Gene prediction | -DNA, DNA polymorphism, Genetics | -SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. | -The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. | -- | Up-to-date | -https://github.com/KorfLab/SNAP | -Sequence Analysis | -snap | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap | -
- | sniffles | -1.0.12 | -2.2 | -sniffles | -To update | -sniffles | -Sniffles | -Sequence analysis, Structural variation detection | -DNA structural variation, Sequencing | -Galaxy wrapper for sniffles | -An algorithm for structural variation detection from third generation sequencing alignment. | -- | To update | -https://github.com/fritzsedlazeck/Sniffles | -Sequence Analysis | -sniffles | -iuc | -https://github.com/galaxyproject/tools-iuc | -
- | snipit | -1.2 | -1.2 | -snipit | -Up-to-date | -snipit | -snipit | -Base position variability plotting | -Virology | -Summarise snps relative to a reference sequence | -Summarise snps relative to a reference sequence | -- | Up-to-date | -https://github.com/aineniamh/snipit | -Variant Analysis, Sequence Analysis | -snipit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit | -
- | snippy | -- | 4.6.0 | -snippy | -To update | -snippy | -snippy | -Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling | -Genomics, Model organisms, DNA polymorphism, Phylogenetics | -Contains the snippy tool for characterising microbial snps | -Rapid haploid variant calling and core SNP phylogeny generation. | -- | To update | -https://github.com/tseemann/snippy | -Sequence Analysis | -snippy | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy | -
- | snp-dists | -0.8.2 | -0.8.2 | -snp-dists | -Up-to-date | -- | - | - | - | Compute pairwise SNP distance matrix from a FASTA sequence alignment | -- | - | Up-to-date | -https://github.com/tseemann/snp-dists | -Variant Analysis | -snp_dists | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists | -
- | snp-sites | -2.5.1 | -2.5.1 | -snp-sites | -Up-to-date | -- | - | - | - | Finds SNP sites from a multi-FASTA alignment file | -- | - | Up-to-date | -https://github.com/sanger-pathogens/snp-sites | -Variant Analysis | -snp_sites | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites | -
- | snpeff-covid19 | -- | - | - | To update | -snpeff | -snpEff | -SNP detection | -DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs | -SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox | -Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). | -- | To update | -http://snpeff.sourceforge.net/ | -Genome-Wide Association Study, Variant Analysis | -snpeff_sars_cov_2 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff | -
- | snpfreqplot | -1.0 | -- | r-base | -To update | -- | - | - | - | Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data | -- | - | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ | -Variant Analysis | -snpfreqplot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ | -
- | socru | -2.1.7 | -2.2.4 | -socru | -To update | -- | - | - | - | Order and orientation of complete bacterial genomes | -- | - | To update | -https://github.com/quadram-institute-bioscience/socru | -Sequence Analysis | -socru | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru | -
- | sonneityping | -20210201 | -20210201 | -sonneityping | -Up-to-date | -- | - | - | - | Scripts for parsing Mykrobe predict results for Shigella sonnei. | -- | - | Up-to-date | -https://github.com/katholt/sonneityping | -Sequence Analysis | -sonneityping | -iuc | -https://github.com/katholt/sonneityping | -
- | spades | -3.15.5 | -3.15.5 | -spades | -Up-to-date | -biosyntheticspades | -biosyntheticSPAdes | -Sequence assembly | -Sequence assembly, Sequence sites, features and motifs, Genetic engineering | -SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. | -biosyntheticSPAdes - biosynthetic gene cluster assembly with paired-end reads | -- | Up-to-date | -https://github.com/ablab/spades | -Assembly, RNA, Metagenomics | -spades | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades | -
- | spaln | -2.4.9 | -- | python | -To update | -- | - | - | - | Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. | -- | - | To update | -http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ | -Sequence Analysis, Genome annotation | -spaln | -iuc | -https://github.com/ogotoh/spaln | -
- | spotyping | -2.1 | -2.1 | -spotyping | -Up-to-date | -spotyping | -SpoTyping | -Variant pattern analysis | -Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation | -SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads | -Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. | -- | Up-to-date | -https://github.com/xiaeryu/SpoTyping-v2.0 | -Sequence Analysis | -spotyping | -iuc | -https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine | -
- | spyboat | -0.1.2 | -- | spyboat | -To update | -- | - | - | - | Wavelet analysis for 3d-image stacks | -- | - | To update | -http://github.com/tensionhead/spyboat | -Imaging, Graphics | -spyboat | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat | -
- | sra-tools | -3.0.8 | -3.0.10 | -sra-tools | -To update | -sra-tools | -SRA Software Toolkit | -Data handling | -DNA, Genomics, Sequencing | -NCBI Sequence Read Archive toolkit utilities | -The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | -- | To update | -https://github.com/ncbi/sra-tools | -Data Source, Fastq Manipulation | -sra_tools | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools | -
- | srst2 | -0.2.0 | -1.19.2 | -samtools | -To update | -- | - | - | - | SRST2 Short Read Sequence Typing for Bacterial Pathogens | -- | - | To update | -http://katholt.github.io/srst2/ | -Metagenomics | -srst2 | -iuc | -https://github.com/katholt/srst2 | -
- | stacks | -- | 2.65 | -stacks | -To update | -stacks | -Stacks | -Data handling | -Mapping, Population genetics | -Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq | -Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. | -- | To update | -http://catchenlab.life.illinois.edu/stacks/ | -Sequence Analysis | -stacks | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks | -
- | stacks2 | -2.55 | -2.65 | -stacks | -To update | -- | - | - | - | Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq | -- | - | To update | -http://catchenlab.life.illinois.edu/stacks/ | -Sequence Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 | -
- | star_fusion | -0.5.4-3+galaxy1 | -1.12.0 | -star-fusion | -To update | -- | - | - | - | STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR | -- | - | To update | -- | Sequence Analysis, Transcriptomics | -star_fusion | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion | -
- | straindesign | -3.2.2 | -3.2.2 | -straindesign | -Up-to-date | -- | - | - | - | Toolbox to optimize biological model | -- | - | Up-to-date | -https://github.com/brsynth/straindesign | -Systems Biology, Synthetic Biology | -straindesign | -iuc | -https://github.com/brsynth/straindesign | -
- | strelka | -2.9.10 | -2.9.10 | -strelka | -Up-to-date | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/Illumina/strelka/ | -Variant Analysis | -strelka | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka | -
- | stringtie | -2.2.1 | -2.2.1 | -stringtie | -Up-to-date | -stringtie | -StringTie | -Transcriptome assembly, RNA-Seq analysis | -Transcriptomics, RNA-seq | -StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. | -Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. | -- | Up-to-date | -http://ccb.jhu.edu/software/stringtie/ | -Transcriptomics | -stringtie | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie | -
- | structure | -2.3.4 | -2.3.4 | -structure | -Up-to-date | -structure | -Structure | -Genetic variation analysis | -Population genetics | -for using multi-locus genotype data to investigate population structure. | -The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. | -- | Up-to-date | -- | Phylogenetics, Variant Analysis | -structure | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure | -
- | structureharvester | -0.6.94 | -0.6.94 | -structureharvester | -Up-to-date | -- | - | - | - | for parsing STRUCTURE outputs and for performing the Evanno method | -- | - | Up-to-date | -- | Phylogenetics, Variant Analysis | -structureharvester | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester | -
- | swift | -1.0 | -1.0 | -swiftlink | -Up-to-date | -- | - | - | - | Parallel MCMC Linkage Analysis | -- | - | Up-to-date | -https://github.com/ajm/swiftlink | -Variant Analysis | -swiftlink | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ | -
- | syndiva | -1.0 | -- | clustalo | -To update | -- | - | - | - | SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. | -- | - | To update | -- | Proteomics | -syndiva | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA | -
- | table_compute | -1.2.4 | -- | pandas | -To update | -- | - | - | - | Perform general-purpose table operations | -- | - | To update | -- | Text Manipulation | -table_compute | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute | -
- | tag_pileup_frequency | -1.0.2 | -- | openjdk | -To update | -- | - | - | - | Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. | -- | - | To update | -https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup | -Statistics, SAM, Genomic Interval Operations | -tag_pileup_frequency | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency | -
- | tasmanian_mismatch | -1.0.7 | -1.0.7 | -tasmanian-mismatch | -Up-to-date | -- | - | - | - | Analysis of positional mismatches | -- | - | Up-to-date | -- | Sequence Analysis | -tasmanian_mismatch | -iuc | -https://github.com/nebiolabs/tasmanian-mismatch | -
- | taxonomy_filter_refseq | -0.3.0 | -1.0.7 | -rust-ncbitaxonomy | -To update | -- | - | - | - | Filter RefSeq by taxonomy | -- | - | To update | -https://github.com/pvanheus/ncbitaxonomy | -Sequence Analysis, Genome annotation | -taxonomy_filter_refseq | -iuc | -https://github.com/galaxyproject/tools-iuc | -
- | taxonomy_krona_chart | -2.7.1+galaxy0 | -2.8.1 | -krona | -To update | -krona | -Krona | -Visualisation | -Metagenomics | -Krona pie chart from taxonomic profile | -Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). | -- | To update | -http://sourceforge.net/projects/krona/ | -Assembly | -taxonomy_krona_chart | -crs4 | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart | -
- | tb-profiler | -4.4.1 | -5.0.1 | -tb-profiler | -To update | -- | - | - | - | Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. | -- | - | To update | -https://github.com/jodyphelan/TBProfiler | -Sequence Analysis | -tbprofiler | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler | -
- | tb_variant_filter | -0.4.0 | -0.4.0 | -tb_variant_filter | -Up-to-date | -- | - | - | - | M. tuberculosis H37Rv VCF filter | -- | - | Up-to-date | -https://github.com/COMBAT-TB/tb_variant_filter | -Variant Analysis | -tb_variant_filter | -iuc | -https://github.com/COMBAT-TB/tb_variant_filter | -
- | tbl2gff3 | -1.2 | -0.6.6 | -bcbiogff | -To update | -- | - | - | - | Table to GFF3 | -- | - | To update | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 | -Convert Formats, Sequence Analysis | -tbl2gff3 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 | -
- | tbvcfreport | -0.1.10 | -0.1.10 | -tbvcfreport | -Up-to-date | -- | - | - | - | Generate HTML report from SnpEff M.tuberculosis VCF(s) | -- | - | Up-to-date | -https://github.com/COMBAT-TB/tbvcfreport | -Variant Analysis | -tbvcfreport | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport | -
- | te_finder | -1.0.1 | -1.19.2 | -samtools | -To update | -tefinder | -TEfinder | -Genome indexing, Variant calling, PCR primer design | -Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation | -Transposable element insertions finder | -A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. | -- | To update | -https://github.com/VistaSohrab/TEfinder | -Sequence Analysis | -te_finder | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ | -
- | telescope | -1.0.3 | -1.0.3 | -telescope | -Up-to-date | -Telescope-expression | -Telescope | -Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping | -RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly | -Single locus resolution of Transposable ELEment expression. | -Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. | -- | Up-to-date | -https://github.com/mlbendall/telescope/ | -Genome annotation | -telescope_assign | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope | -
- | tetoolkit | -2.2.3 | -2.2.3 | -tetranscripts | -Up-to-date | -- | - | - | - | The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. | -- | - | Up-to-date | -http://hammelllab.labsites.cshl.edu/software/ | -Sequence Analysis | -tetoolkit | -iuc | -https://github.com/mhammell-laboratory/TEtranscripts | -
- | tetyper | -1.1 | -1.1 | -tetyper | -Up-to-date | -- | - | - | - | Type a specific transposable element (TE) of interest from paired-end sequencing data. | -- | - | Up-to-date | -https://github.com/aesheppard/TETyper | -Sequence Analysis | -tetyper | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper | -
- | tn93 | -1.0.6 | -1.0.13 | -tn93 | -To update | -- | - | - | - | Compute distances between sequences | -- | - | To update | -https://github.com/veg/tn93/ | -Sequence Analysis | -tn93 | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ | -
- | tracy | -0.6.1 | -0.7.6 | -tracy | -To update | -- | - | - | - | - | - | - | To update | -- | - | - | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy | -
- | transdecoder | -5.5.0 | -5.7.1 | -transdecoder | -To update | -TransDecoder | -TransDecoder | -Coding region prediction, de Novo sequencing, De-novo assembly | -Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing | -TransDecoder finds coding regions within transcripts | -TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. | -- | To update | -https://transdecoder.github.io/ | -Transcriptomics, RNA | -transdecoder | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder | -
- | transit | -3.0.2 | -3.2.3 | -transit | -To update | -transit | -TRANSIT | -Transposon prediction | -DNA, Sequencing, Mobile genetic elements | -TRANSIT | -A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. | -- | To update | -https://github.com/mad-lab/transit/ | -Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ | -
- | transtermhp | -- | 2.09 | -transtermhp | -To update | -- | - | - | - | Finds rho-independent transcription terminators in bacterial genomes | -- | - | To update | -- | Sequence Analysis | -transtermhp | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp | -
- | trimmomatic | -0.39 | -0.39 | -trimmomatic | -Up-to-date | -- | - | - | - | A flexible read trimming tool for Illumina NGS data | -- | - | Up-to-date | -http://www.usadellab.org/cms/?page=trimmomatic | -Fastq Manipulation | -trimmomatic | -pjbriggs | -https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic | -
- | trinity | -2.15.1 | -2.15.1 | -trinity | -Up-to-date | -trinity | -Trinity | -Transcriptome assembly | -Transcriptomics, Gene expression, Gene transcripts | -Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq | -Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. | -- | Up-to-date | -https://github.com/trinityrnaseq/trinityrnaseq | -Transcriptomics, RNA | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity | -
- | trinotate | -3.2.2 | -4.0.2 | -trinotate | -To update | -trinotate | -Trinotate | -Gene functional annotation | -Gene expression, Transcriptomics | -Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. | -Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. | -- | To update | -https://trinotate.github.io/ | -Transcriptomics, RNA | -trinotate | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate | -
- | trycycler | -0.5.4 | -0.5.4 | -trycycler | -Up-to-date | -- | - | - | - | Trycycler toolkit wrappers | -- | - | Up-to-date | -https://github.com/rrwick/Trycycler | -Assembly | -trycycler | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler | -
- | tsebra | -1.1.2.3 | -1.1.2.3 | -tsebra | -Up-to-date | -- | - | - | - | This tool has been developed to combine BRAKER predictions. | -- | - | Up-to-date | -https://github.com/Gaius-Augustus/TSEBRA | -Genome annotation | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra | -
- | tsne | -0.0.2 | -0.13 | -r-rtsne | -To update | -- | - | - | - | T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation | -- | - | To update | -https://cran.r-project.org/web/packages/Rtsne/ | -Text Manipulation | -tsne | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne | -
- | tximport | -1.22.0 | -1.30.0 | -bioconductor-tximport | -To update | -tximport | -tximport | -Pathway or network analysis, Formatting, RNA-Seq analysis | -Transcriptomics, Gene transcripts, Workflows | -Wrapper for the Bioconductor package tximport | -An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. | -- | To update | -http://bioconductor.org/packages/tximport/ | -Transcriptomics | -tximport | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport | -
- | ucsc_blat | -377 | -445 | -ucsc-blat | -To update | -blat | -BLAT | -Sequence alignment | -Sequence analysis | -Standalone blat sequence search command line tool | -Fast, accurate spliced alignment of DNA sequences. | -- | To update | -http://genome.ucsc.edu/goldenPath/help/blatSpec.html | -Sequence Analysis | -ucsc_blat | -yating-l | -- |
- | fasplit | -377 | -377 | -ucsc-fasplit | -Up-to-date | -UCSC_Genome_Browser_Utilities | -UCSC Genome Browser Utilities | -- | Sequence analysis | -faSplit is a tool to split a single FASTA file into several files | -Utilities for handling sequences and assemblies from the UCSC Genome Browser project. | -- | Up-to-date | -http://hgdownload.cse.ucsc.edu/admin/exe/ | -Fasta Manipulation | -ucsc_fasplit | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit | -
- | fatovcf | -448 | -448 | -ucsc-fatovcf | -Up-to-date | -UCSC_Genome_Browser_Utilities | -UCSC Genome Browser Utilities | -- | Sequence analysis | -Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs | -Utilities for handling sequences and assemblies from the UCSC Genome Browser project. | -- | Up-to-date | -http://hgdownload.cse.ucsc.edu/admin/exe/ | -Convert Formats | -ucsc_fatovcf | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf | -
- | twobittofa | -377 | -455 | -ucsc-twobittofa | -To update | -UCSC_Genome_Browser_Utilities | -UCSC Genome Browser Utilities | -- | Sequence analysis | -twoBitToFa is a tool to convert all or part of .2bit file to FASTA | -Utilities for handling sequences and assemblies from the UCSC Genome Browser project. | -- | To update | -https://genome.ucsc.edu/goldenpath/help/twoBit.html | -Convert Formats | -ucsc_twobittofa | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa | -
- | wigtobigwig | -447 | -447 | -ucsc-wigtobigwig | -Up-to-date | -UCSC_Genome_Browser_Utilities | -UCSC Genome Browser Utilities | -- | Sequence analysis | -converts bedGraph (wig) files into binary bigwig | -Utilities for handling sequences and assemblies from the UCSC Genome Browser project. | -- | Up-to-date | -https://genome.ucsc.edu/goldenPath/help/bigWig.html | -Convert Formats | -ucsc_wigtobigwig | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig | -
- | umi_tools | -1.1.2 | -1.1.5 | -umi_tools | -To update | -umi-tools | -UMI-tools | -Sequencing quality control | -NGS, Sequence sites, features and motifs, Quality affairs | -UMI-tools extract - Extract UMIs from fastq | -Tools for handling Unique Molecular Identifiers in NGS data sets. | -- | To update | -https://github.com/CGATOxford/UMI-tools | -Sequence Analysis, Transcriptomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools | -
- | unicycler | -0.5.0 | -0.5.0 | -unicycler | -Up-to-date | -unicycler | -Unicycler | -Genome assembly, Aggregation | -Microbiology, Genomics, Sequencing, Sequence assembly | -Unicycler is a hybrid assembly pipeline for bacterial genomes. | -A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. | -- | Up-to-date | -https://github.com/rrwick/Unicycler | -Assembly | -unicycler | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler | -
- | usher | -0.2.1 | -0.6.3 | -usher | -To update | -- | - | - | - | UShER toolkit wrappers | -- | - | To update | -https://github.com/yatisht/usher | -Phylogenetics | -usher | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher | -
- | valet | -- | 1.0 | -valet | -To update | -- | - | - | - | A pipeline for detecting mis-assemblies in metagenomic assemblies. | -- | - | To update | -https://github.com/marbl/VALET | -Metagenomics | -valet | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet | -
- | vapor | -1.0.2 | -1.0.2 | -vapor | -Up-to-date | -vapor | -VAPOR | -Data retrieval, De-novo assembly, Read mapping | -Whole genome sequencing, Mapping, Sequence assembly | -Classify Influenza samples from raw short read sequence data | -VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. | -- | Up-to-date | -https://github.com/connor-lab/vapor | -Sequence Analysis | -vapor | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor | -
- | vardict | -1.8.3 | -- | python | -To update | -- | - | - | - | VarDict - calls SNVs and indels for tumour-normal pairs | -- | - | To update | -https://github.com/AstraZeneca-NGS/VarDictJava | -Variant Analysis | -vardict_java | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict | -
- | variant_analyzer | -2.0.0 | -- | matplotlib | -To update | -- | - | - | - | Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data | -- | - | To update | -- | Variant Analysis | -variant_analyzer | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer | -
- | varscan | -2.4.3 | -2.4.6 | -varscan | -To update | -- | - | - | - | VarScan is a variant caller for high-throughput sequencing data | -- | - | To update | -https://dkoboldt.github.io/varscan/ | -Variant Analysis | -varscan | -iuc | -https://github.com/galaxyproject/iuc/tree/master/tools/varscan | -
- | varvamp | -1.1.1 | -1.1.1 | -varvamp | -Up-to-date | -varvamp | -varVAMP | -PCR primer design | -Virology | -Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses | -variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. | -- | Up-to-date | -https://github.com/jonas-fuchs/varVAMP/ | -Sequence Analysis | -varvamp | -iuc | -https://github.com/jonas-fuchs/varVAMP | -
- | vcf2maf | -1.6.21 | -1.6.21 | -vcf2maf | -Up-to-date | -- | - | - | - | vcf2maf: Convert VCF into MAF | -- | - | Up-to-date | -- | Convert Formats | -vcf2maf | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf | -
- | vcfanno | -0.3.5 | -0.3.5 | -vcfanno | -Up-to-date | -vcfanno | -vcfanno | -SNP annotation | -Genetic variation, Data submission, annotation and curation | -Annotate VCF files | -Fast, flexible annotation of genetic variants. | -- | Up-to-date | -https://github.com/brentp/vcfanno | -Variant Analysis | -vcfanno | -iuc | -https://github.com/galaxyproject/tools-iuc/vcfanno/ | -
- | vegan | -2.4-3 | -2.3_4 | -r-vegan | -To update | -- | - | - | - | - | - | - | To update | -https://cran.r-project.org/package=vegan | -Metagenomics | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ | -
- | velocyto | -0.17.17 | -0.17.17 | -velocyto.py | -Up-to-date | -- | - | - | - | Velocyto is a library for the analysis of RNA velocity. | -- | - | Up-to-date | -http://velocyto.org/ | -Transcriptomics | -velocyto | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto | -
- | velvet | -- | 1.2.10 | -velvet | -To update | -velvet | -Velvet | -Formatting, De-novo assembly | -Sequence assembly | -de novo genomic assembler specially designed for short read sequencing technologies | -A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. | -- | To update | -https://www.ebi.ac.uk/~zerbino/velvet/ | -Assembly | -velvet | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet | -
- | velvet_optimiser | -2.2.6+galaxy2 | -1.2.10 | -velvet | -To update | -velvetoptimiser | -VelvetOptimiser | -Optimisation and refinement, Sequence assembly | -Genomics, Sequence assembly | -Automatically optimize Velvet assemblies | -This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. | -- | To update | -- | Assembly | -velvetoptimiser | -simon-gladman | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser | -
- | verkko | -1.3.1 | -2.0 | -verkko | -To update | -- | - | - | - | Telomere-to-telomere assembly pipeline | -- | - | To update | -https://github.com/marbl/verkko | -Assembly | -verkko | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko | -
- | vg | -1.23.0 | -1.55.0 | -vg | -To update | -- | - | - | - | Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods | -- | - | To update | -https://github.com/vgteam/vg | -Sequence Analysis, Variant Analysis | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg | -
- | virhunter | -1.0.0 | -- | numpy | -To update | -virhunter | -VirHunter | -Sequence classification | -Virology | -Deep Learning method for novel virus detection in sequencing data | -VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). | -- | To update | -https://github.com/cbib/virhunter | -Machine Learning | -virhunter | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter | -
- | volcanoplot | -0.0.5 | -2.2.1 | -r-ggplot2 | -To update | -- | - | - | - | Tool to create a Volcano Plot | -- | - | To update | -- | Visualization, Transcriptomics, Statistics | -volcanoplot | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot | -
- | vsearch | -2.8.3 | -2.27.0 | -vsearch | -To update | -vsearch | -VSEARCH | -DNA mapping, Chimera detection | -Metagenomics, Sequence analysis | -VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. | -High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. | -- | To update | -https://github.com/torognes/vsearch | -Sequence Analysis | -vsearch | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch | -
- | vsnp | -3.0.6 | -0.22.0 | -pysam | -To update | -- | - | - | - | The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. | -- | - | To update | -https://github.com/USDA-VS/vSNP | -Sequence Analysis | -vsnp | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp | -
- | weather_app | -0.1.2 | -- | curl | -To update | -- | - | - | - | provides simple weather in text format | -- | - | To update | -http://wttr.in/ | -Visualization, Web Services | -simpleweather | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app | -
- | weblogo3 | -3.5.0 | -3.7.9 | -weblogo | -To update | -weblogo | -WebLogo | -Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition | -Nucleic acid sites, features and motifs, Sequence analysis | -Sequence Logo generator for fasta | -Web-based application designed to make generate sequence logos. | -- | To update | -- | Graphics | -weblogo3 | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 | -
- | windowmasker | -1.0 | -2.15.0 | -blast | -To update | -- | - | - | - | Identify repetitive regions using WindowMasker | -- | - | To update | -https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ | -Sequence Analysis | -windowmasker | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ | -
- | winnowmap | -2.03 | -2.03 | -winnowmap | -Up-to-date | -- | - | - | - | A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. | -- | - | Up-to-date | -https://github.com/marbl/Winnowmap | -Next Gen Mappers | -winnowmap | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap | -
- | xpath | -- | 1.47 | -perl-xml-xpath | -To update | -- | - | - | - | XPath XML querying tool | -- | - | To update | -http://search.cpan.org/dist/XML-XPath/ | -Text Manipulation | -xpath | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath | -
- | yahs | -1.2a.2 | -1.2a.2 | -yahs | -Up-to-date | -- | - | - | - | Yet Another Hi-C scaffolding tool | -- | - | Up-to-date | -https://github.com/c-zhou/yahs | -Assembly | -yahs | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs | -
- | zerone | -1.0 | -1.0 | -zerone | -Up-to-date | -- | - | - | - | ChIP-seq discretization and quality control | -- | - | Up-to-date | -https://github.com/nanakiksc/zerone | -ChIP-seq | -zerone | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone | -
- | bamtools | -2.5.2 | -2.5.2 | -bamtools | -Up-to-date | -- | - | - | - | Operate on and transform BAM datasets in various ways using bamtools | -- | - | Up-to-date | -https://github.com/pezmaster31/bamtools | -Sequence Analysis, SAM | -bamtools | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools | -
- | bamtools_filter | -2.5.2 | -2.5.2 | -bamtools | -Up-to-date | -- | - | - | - | Filter BAM datasets on various attributes using bamtools filter | -- | - | Up-to-date | -https://github.com/pezmaster31/bamtools | -Sequence Analysis, SAM | -bamtools_filter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter | -
- | bamtools_split | -2.5.2 | -2.5.2 | -bamtools | -Up-to-date | -- | - | - | - | - | - | - | Up-to-date | -https://github.com/pezmaster31/bamtools | -Sequence Analysis, SAM | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split | -
- | biotradis | -1.4.5 | -1.4.5 | -biotradis | -Up-to-date | -- | - | - | - | Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. | -- | - | Up-to-date | -https://www.sanger.ac.uk/science/tools/bio-tradis | -Genome annotation | -biotradis | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis | -
- | cuffcompare | -2.2.1 | -2.2.1 | -cufflinks | -Up-to-date | -- | - | - | - | Galaxy wrappers for the Cuffcompare tool. | -- | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cuffcompare | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare | -
- | cuffdiff | -2.2.1 | -2.2.1 | -cufflinks | -Up-to-date | -- | - | - | - | Galaxy wrappers for the Cuffdiff tool. | -- | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cuffdiff | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff | -
- | cufflinks | -2.2.1 | -2.2.1 | -cufflinks | -Up-to-date | -- | - | - | - | Galaxy wrappers for the Cufflinks tool. | -- | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cufflinks | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks | -
- | cuffmerge | -2.2.1 | -2.2.1 | -cufflinks | -Up-to-date | -- | - | - | - | Galaxy wrappers for the Cuffmerge tool. | -- | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cuffmerge | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge | -
- | cuffnorm | -2.2.1 | -2.2.1 | -cufflinks | -Up-to-date | -- | - | - | - | The Cuffnorm tool | -- | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cuffnorm | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm | -
- | cuffquant | -2.2.1 | -2.2.1 | -cufflinks | -Up-to-date | -- | - | - | - | The Cuffquant tool | -- | - | Up-to-date | -http://cole-trapnell-lab.github.io/cufflinks/ | -Transcriptomics | -cuffquant | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant | -
- | fasta_clipping_histogram | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Length Distribution chart | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Graphics, Statistics | -fasta_clipping_histogram | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram | -
- | fasta_formatter | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | FASTA Width formatter | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation | -fasta_formatter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter | -
- | fasta_nucleotide_changer | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | RNA/DNA converter. | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation | -fasta_nucleotide_changer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer | -
- | fastq_quality_boxplot | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Draw quality score boxplot | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation, Graphics, Statistics | -fastq_quality_boxplot | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot | -
- | fastq_quality_converter | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Quality format converter (ASCII-Numeric) | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation | -fastq_quality_converter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter | -
- | fastq_quality_filter | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Filter by quality | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation | -fastq_quality_filter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter | -
- | fastq_to_fasta | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | FASTQ to FASTA converter | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Convert Formats | -fastq_to_fasta | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta | -
- | fastx_artifacts_filter | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Remove sequencing artifacts | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Fastq Manipulation | -fastx_artifacts_filter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter | -
- | fastx_barcode_splitter | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Barcode Splitter | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Fastq Manipulation | -fastx_barcode_splitter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter | -
- | fastx_clipper | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Clip adapter sequences | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Fastq Manipulation | -fastx_clipper | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper | -
- | fastx_collapser | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Collapse sequences | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation | -fastx_collapser | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser | -
- | fastx_nucleotides_distribution | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Draw nucleotides distribution chart | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation, Graphics | -fastx_nucleotides_distribution | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution | -
- | fastx_quality_statistics | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Compute quality statistics | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation, Statistics | -fastx_quality_statistics | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics | -
- | fastx_renamer | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Rename sequences | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Fastq Manipulation | -fastx_renamer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer | -
- | fastx_reverse_complement | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Reverse-Complement | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fastq Manipulation, Fasta Manipulation | -fastx_reverse_complement | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement | -
- | fastx_trimmer | -0.0.14 | -0.0.14 | -fastx_toolkit | -Up-to-date | -- | - | - | - | Trim sequences | -- | - | Up-to-date | -http://hannonlab.cshl.edu/fastx_toolkit/ | -Fasta Manipulation, Fastq Manipulation | -fastx_trimmer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer | -
- | fastq_combiner | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | Combine FASTA and QUAL into FASTQ | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation, Fasta Manipulation | -fastq_combiner | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner | -
- | fastq_filter | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | Filter FASTQ reads by quality score and length | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_filter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter | -
- | fastq_groomer | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | Convert between various FASTQ quality formats. | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_groomer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer | -
- | fastq_manipulation | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | Manipulate FASTQ reads on various attributes. | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_manipulation | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation | -
- | fastq_masker_by_quality | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | FASTQ Masker by quality score | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_masker_by_quality | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality | -
- | fastq_paired_end_deinterlacer | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | FASTQ de-interlacer on paired end reads. | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_paired_end_deinterlacer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer | -
- | fastq_paired_end_interlacer | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | FASTQ interlacer on paired end reads | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_paired_end_interlacer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer | -
- | fastq_paired_end_joiner | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | FASTQ joiner on paired end reads | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_paired_end_joiner | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner | -
- | fastq_paired_end_splitter | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | FASTQ splitter on joined paired end reads | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_paired_end_splitter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter | -
- | fastq_stats | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | FASTQ Summary Statistics by column | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_stats | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats | -
- | fastq_to_tabular | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | FASTQ to Tabular converter | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_to_tabular | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular | -
- | fastq_trimmer | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | FASTQ Trimmer by quality | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastq_trimmer | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer | -
- | fastqtofasta | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | FASTQ to FASTA converter | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -fastqtofasta | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta | -
- | tabular_to_fastq | -1.1.5 | -1.1.5 | -galaxy_sequence_utils | -Up-to-date | -- | - | - | - | Tabular to FASTQ converter | -- | - | Up-to-date | -https://github.com/galaxyproject/sequence_utils | -Fastq Manipulation | -tabular_to_fastq | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq | -
- | kraken | -- | 1.1.1 | -kraken | -To update | -- | - | - | - | Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. | -- | - | To update | -http://ccb.jhu.edu/software/kraken/ | -Metagenomics | -kraken | -devteam | -https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ | -
- | kraken2 | -2.1.1 | -2.1.3 | -kraken2 | -To update | -kraken2 | -kraken2 | -Taxonomic classification | -Taxonomy, Metagenomics | -Kraken2 for taxonomic designation. | -Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. | -- | To update | -http://ccb.jhu.edu/software/kraken/ | -Metagenomics | -kraken2 | -iuc | -https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ | -
- | samtools | -1.15.1 | -1.19.2 | -samtools | -To update | -- | - | - | - | - | - | - | To update | -https://github.com/samtools/samtools | -SAM | -- | iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools | -
- | snpeff | -- | 1.70 | -biopython | -To update | -- | - | - | - | SnpEff is a genetic variant annotation and effect prediction toolbox | -- | - | To update | -http://snpeff.sourceforge.net/ | -Genome-Wide Association Study, Variant Analysis | -snpeff | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff | -
- | snpsift | -- | 5.2 | -snpsift | -To update | -- | - | - | - | snpEff SnpSift tools from Pablo Cingolani | -- | - | To update | -http://snpeff.sourceforge.net/SnpSift.html | -Variant Analysis | -snpsift | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift | -
- | snpsift_dbnsfp | -- | 5.2 | -snpsift | -To update | -- | - | - | - | snpEff SnpSift dbnsfp tool from Pablo Cingolani | -- | - | To update | -http://snpeff.sourceforge.net/SnpSift.html#dbNSFP | -Variant Analysis | -snpsift_dbnsfp | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp | -
- | snpsift_genesets | -- | 5.2 | -snpsift | -To update | -- | - | - | - | Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome | -- | - | To update | -http://snpeff.sourceforge.net/SnpSift.html#geneSets | -Variant Analysis | -snpsift_genesets | -iuc | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ | -
- | vcf2tsv | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Converts VCF files into tab-delimited format | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis, Convert Formats | -vcf2tsv | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv | -
- | vcfaddinfo | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Adds info fields from the second dataset which are not present in the first dataset. | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfaddinfo | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo | -
- | vcfallelicprimitives | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Splits alleleic primitives (gaps or mismatches) into multiple VCF lines | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfallelicprimitives | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives | -
- | vcfannotate | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Intersect VCF records with BED annotations | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfannotate | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate | -
- | vcfannotategenotypes | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfannotategenotypes | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes | -
- | vcfbedintersect | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Intersect VCF and BED datasets | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfbedintersect | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect | -
- | vcfbreakcreatemulti | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Break multiple alleles into multiple records, or combine overallpoing alleles into a single record | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfbreakcreatemulti | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti | -
- | vcfcheck | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Verify that the reference allele matches the reference genome | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfcheck | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck | -
- | vcfcombine | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Combine multiple VCF datasets | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfcombine | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine | -
- | vcfcommonsamples | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Output records belonging to samples commong between two datasets. | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfcommonsamples | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples | -
- | vcfdistance | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Calculate distance to the nearest variant. | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfdistance | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance | -
- | vcffilter | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Tool for filtering VCF files | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcffilter | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter | -
- | vcffixup | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Count the allele frequencies across alleles present in each record in the VCF file. | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcffixup | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup | -
- | vcfflatten | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Removes multi-allelic sites by picking the most common alternate | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfflatten | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten | -
- | vcfgeno2haplo | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Convert genotype-based phased alleles into haplotype alleles | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfgeno2haplo | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo | -
- | vcfgenotypes | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Convert numerical representation of genotypes to allelic. | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfgenotypes | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes | -
- | vcfhethom | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Count the number of heterozygotes and alleles, compute het/hom ratio. | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfhethom | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom | -
- | vcfleftalign | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Left-align indels and complex variants in VCF dataset | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfleftalign | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign | -
- | vcfprimers | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Extract flanking sequences for each VCF record | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfprimers | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers | -
- | vcfrandomsample | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Randomly sample sites from VCF dataset | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfrandomsample | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample | -
- | vcfselectsamples | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Select samples from a VCF file | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfselectsamples | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples | -
- | vcfsort | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Sort VCF dataset by coordinate | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfsort | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort | -
- | vcfvcfintersect | -- | 1.0.9 | -vcflib | -To update | -- | - | - | - | Intersect two VCF datasets | -- | - | To update | -https://github.com/ekg/vcflib | -Variant Analysis | -vcfvcfintersect | -devteam | -https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect | -
- | ThermoRawFileParser | -1.3.4 | -1.4.3 | -thermorawfileparser | -To update | -- | - | - | - | Thermo RAW file converter | -- | - | To update | -https://github.com/compomics/ThermoRawFileParser | -Proteomics | -thermo_raw_file_converter | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser | -
- | appendfdr | -0.2.0 | -- | - | To update | -- | - | - | - | - | - | - | To update | -- | - | appendfdr | -galaxyp | -- |
- | bed_to_protein_map | -0.2.0 | -- | python | -To update | -- | - | - | - | Converts a BED file to a tabular list of exon locations | -- | - | To update | -- | Proteomics | -bed_to_protein_map | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map | -
- | blast_plus_remote_blastp | -2.6.0 | -2.15.0 | -blast | -To update | -- | - | - | - | NCBI BLAST+ with -remote option | -- | - | To update | -https://blast.ncbi.nlm.nih.gov/ | -Sequence Analysis | -blast_plus_remote_blastp | -galaxyp | -https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus | -
- | bumbershoot | -3.0.21142 | -3_0_21142_0e4f4a4 | -bumbershoot | -To update | -- | - | - | - | - | - | - | To update | -http://proteowizard.sourceforge.net/ | -Proteomics | -- | galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot | -
- | calisp | -3.0.13 | -3.0.13 | -calisp | -Up-to-date | -- | - | - | - | Calgary approach to isotopes in proteomics | -- | - | Up-to-date | -https://github.com/kinestetika/Calisp/ | -Proteomics | -calisp | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp | -
- | cardinal | -2.10.0 | -3.4.3 | -bioconductor-cardinal | -To update | -- | - | - | - | Statistical and computational tools for analyzing mass spectrometry imaging datasets | -- | - | To update | -http://cardinalmsi.org | -Proteomics, Metabolomics | -- | galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal | -
- | dbbuilder | -0.3.4 | -- | wget | -To update | -- | - | - | - | Protein Database Downloader | -- | - | To update | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder | -Proteomics | -dbbuilder | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder | -
- | decoyfasta | -- | - | - | To update | -- | - | - | - | Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. | -- | - | To update | -- | Proteomics | -decoyfasta | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta | -
- | dia_umpire | -2.1.3 | -2.1.6 | -dia_umpire | -To update | -- | - | - | - | DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics | -- | - | To update | -http://diaumpire.sourceforge.net/ | -Proteomics | -dia_umpire | -galaxyp | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire | -
- | dialignr | -1.2.0 | -2.10.0 | -bioconductor-dialignr | -To update | -- | - | - | - | DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. | -- | - | To update | -https://github.com/shubham1637/DIAlignR | -Proteomics | -dialignr | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr | -
- | diann | -1.8.1 | -- | - | To update | -- | - | - | - | DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. | -- | - | To update | -https://github.com/vdemichev/DiaNN | -Proteomics | -diann | -galaxyp | -https://github.com/vdemichev/DiaNN | -
- | diapysef | -0.3.5.0 | -1.0.10 | -diapysef | -To update | -- | - | - | - | diapysef is a convenience package for working with DIA-PASEF data | -- | - | To update | -https://pypi.org/project/diapysef/ | -Proteomics | -diapysef | -galaxyp | -https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef | -
- | diffacto | -1.0.6 | -1.0.6 | -diffacto | -Up-to-date | -- | - | - | - | Diffacto comparative protein abundance estimation | -- | - | Up-to-date | -https://github.com/statisticalbiotechnology/diffacto | -Proteomics | -diffacto | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto | -
- | digestdb | -0.1.0 | -- | trans_proteomic_pipeline | -To update | -- | - | - | - | - | - | - | To update | -- | - | digestdb | -galaxyp | -- |
- | directag_and_tagrecon | -- | - | - | To update | -- | - | - | - | - | - | - | To update | -- | - | directag_and_tagrecon | -galaxyp | -- |
- | data_manager_eggnog_mapper | -- | - | - | To update | -- | - | - | - | downloads eggnog data for eggnog-mapper | -- | - | To update | -- | Proteomics | -data_manager_eggnog_mapper | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager | -
- | data_manager_eggnog_mapper_abspath | -- | - | - | To update | -- | - | - | - | download eggnog data for eggnog-mapper | -- | - | To update | -- | Proteomics | -data_manager_eggnog_mapper_abspath | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath | -
- | eggnog_mapper | -2.1.8 | -2.1.12 | -eggnog-mapper | -To update | -eggnog-mapper-v2 | -eggNOG-mapper v2 | -Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval | -Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis | -eggnog-mapper fast functional annotation of novel sequences | -EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. | -- | To update | -- | Proteomics | -eggnog_mapper | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper | -
- | encyclopedia | -1.12.34 | -2.12.30 | -encyclopedia | -To update | -- | - | - | - | Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis | -- | - | To update | -https://bitbucket.org/searleb/encyclopedia/wiki/Home | -Proteomics | -encyclopedia | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia | -
- | fasta_merge_files_and_filter_unique_sequences | -1.2.0 | -- | python | -To update | -- | - | - | - | Concatenate FASTA database files together | -- | - | To update | -https://github.com/galaxyproteomics/tools-galaxyp/ | -Fasta Manipulation | -fasta_merge_files_and_filter_unique_sequences | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences | -
- | fastg2protlib | -1.0.2 | -- | - | To update | -- | - | - | - | Generate FASTA from FASTG | -- | - | To update | -https://github.com/galaxyproteomics/fastg2protlib.git | -Proteomics | -fastg2protlib | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib | -
- | feature_alignment | -0.11.0 | -0.11.0 | -msproteomicstools | -Up-to-date | -- | - | - | - | TRIC integrates information from all available runs via a graph-based alignment strategy | -- | - | Up-to-date | -- | Proteomics | -feature_alignment | -galaxyp | -https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md | -
- | filter_by_fasta_ids | -2.3 | -- | python | -To update | -- | - | - | - | Filter FASTA on the headers and/or the sequences | -- | - | To update | -- | Fasta Manipulation, Proteomics | -filter_by_fasta_ids | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids | -
- | flashlfq | -1.0.3.1 | -1.2.6 | -flashlfq | -To update | -- | - | - | - | FlashLFQ mass-spectrometry proteomics label-free quantification | -- | - | To update | -https://github.com/smith-chem-wisc/FlashLFQ | -Proteomics | -flashlfq | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq | -
- | gffcompare_to_bed | -0.2.1 | -- | python | -To update | -- | - | - | - | Filter and convert a gffCompare GTF to BED | -- | - | To update | -https://github.com/gpertea/gffcompare/ | -Convert Formats | -gffcompare_to_bed | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed | -
- | hardklor | -2.30.1+galaxy1 | -2.3.2 | -hardklor | -To update | -- | - | - | - | Hardklör | -- | - | To update | -- | Proteomics | -hardklor | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor | -
- | idconvert | -- | 3_0_9992 | -proteowizard | -To update | -- | - | - | - | Convert mass spectrometry identification files on linux or MacOSX | -- | - | To update | -- | Proteomics | -idconvert | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert | -
- | lfq_protein_quant | -1.0 | -2.28.1 | -bioconductor-msnbase | -To update | -- | - | - | - | Enable protein summarisation and quantitation | -- | - | To update | -https://github.com/compomics/LFQ_galaxy_p | -Proteomics | -lfq_protein_quant | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant | -
- | ltq_iquant_cli | -- | - | - | To update | -- | - | - | - | - | - | - | To update | -- | - | ltq_iquant_cli | -galaxyp | -- |
- | maldiquant | -1.22.0 | -- | r-base | -To update | -- | - | - | - | MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. | -- | - | To update | -http://strimmerlab.org/software/maldiquant/ | -Proteomics | -MALDIquant | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant | -
- | map_peptides_to_bed | -0.2 | -1.70 | -biopython | -To update | -- | - | - | - | Map peptides to a reference genome for display by a genome browser | -- | - | To update | -- | Proteomics | -map_peptides_to_bed | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed | -
- | maxquant | -2.0.3.0 | -2.0.3.0 | -maxquant | -Up-to-date | -- | - | - | - | wrapper for MaxQuant | -- | - | Up-to-date | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant | -Proteomics | -maxquant | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant | -
- | meta_proteome_analyzer | -2.0.0 | -2.0.0 | -mpa-portable | -Up-to-date | -- | - | - | - | MetaProteomeAnalyzer | -- | - | Up-to-date | -https://github.com/compomics/meta-proteome-analyzer/ | -Proteomics | -meta_proteome_analyzer | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer | -
- | metagene_annotator | -1.0.0 | -1.0 | -metagene_annotator | -To update | -- | - | - | - | MetaGeneAnnotator gene-finding program for prokaryote and phage | -- | - | To update | -- | Sequence Analysis | -metagene_annotator | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator | -
- | metanovo | -1.9.4 | -1.9.4 | -metanovo | -Up-to-date | -- | - | - | - | Produce targeted databases for mass spectrometry analysis. | -- | - | Up-to-date | -https://github.com/uct-cbio/proteomics-pipelines | -Proteomics | -metanovo | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo | -
- | metaquantome | -2.0.2 | -2.0.2 | -metaquantome | -Up-to-date | -- | - | - | - | quantitative analysis of microbiome taxonomy and function | -- | - | Up-to-date | -https://github.com/galaxyproteomics/metaquantome/ | -Proteomics | -metaquantome | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome | -
- | mgf_formatter | -1.0.0 | -1.0.0 | -mgf-formatter | -Up-to-date | -- | - | - | - | - | - | - | Up-to-date | -- | - | mgf_formatter | -galaxyp | -- |
- | moFF | -2.0.3 | -2.0.3 | -moff | -Up-to-date | -- | - | - | - | moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. | -- | - | Up-to-date | -https://github.com/compomics/moFF | -Proteomics | -proteomics_moff | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF | -
- | morpheus | -2.255.0 | -287 | -morpheus | -To update | -- | - | - | - | Morpheus MS Search Application | -- | - | To update | -- | Proteomics | -morpheus | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus | -
- | mqppep | -0.1.19 | -1.64.0 | -bioconductor-preprocesscore | -To update | -- | - | - | - | MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA | -- | - | To update | -https://github.com/galaxyproteomics/tools-galaxyp/ | -Proteomics | -mqppep | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep | -
- | msconvert | -3.0.20287 | -- | - | To update | -- | - | - | - | msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container | -- | - | To update | -- | Proteomics | -msconvert | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert | -
- | msgfplus | -0.5 | -2023.01.1202 | -msgf_plus | -To update | -- | - | - | - | MSGF+ | -- | - | To update | -- | Proteomics | -msgfplus | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus | -
- | msms_extractor | -1.0.0 | -3_0_9992 | -proteowizard | -To update | -- | - | - | - | Extract MS/MS scans from the mzML file(s) based on PSM report. | -- | - | To update | -- | Proteomics | -msms_extractor | -galaxyp | -- |
- | msstats | -4.0.0 | -4.10.0 | -bioconductor-msstats | -To update | -- | - | - | - | MSstats tool for analyzing mass spectrometry proteomic datasets | -- | - | To update | -https://github.com/MeenaChoi/MSstats | -Proteomics | -- | galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats | -
- | msstatstmt | -2.0.0 | -2.10.0 | -bioconductor-msstatstmt | -To update | -- | - | - | - | MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling | -- | - | To update | -http://msstats.org/msstatstmt/ | -Proteomics | -msstatstmt | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt | -
- | mt2mq | -1.1.0 | -- | r-tidyverse | -To update | -- | - | - | - | Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome | -- | - | To update | -- | Proteomics | -mt2mq | -galaxyp | -- |
- | mz_to_sqlite | -2.1.1+galaxy0 | -2.1.1 | -mztosqlite | -To update | -- | - | - | - | Creates a SQLite database for proteomics data | -- | - | To update | -- | Proteomics | -mz_to_sqlite | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite | -
- | openms | -2.8 | -3.1.0 | -openms | -To update | -- | - | - | - | OpenMS Suite for LC/MS data management and analyses | -- | - | To update | -https://www.openms.de/ | -Proteomics | -openms | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms | -
- | pathwaymatcher | -- | 1.9.1 | -pathwaymatcher | -To update | -- | - | - | - | Reactome Pathway Matcher | -- | - | To update | -https://github.com/LuisFranciscoHS/PathwayMatcher | -Proteomics | -reactome_pathwaymatcher | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher | -
- | pep_pointer | -0.1.3+galaxy1 | -- | python | -To update | -- | - | - | - | PepPointer categorizes peptides by their genomic coordinates. | -- | - | To update | -- | Genomic Interval Operations, Proteomics | -pep_pointer | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer | -
- | pepquery | -1.6.2 | -2.0.2 | -pepquery | -To update | -- | - | - | - | A peptide-centric MS search engine for novel peptide identification and validation. | -- | - | To update | -https://pepquery.org | -Proteomics | -pepquery | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery | -
- | pepquery2 | -2.0.2 | -2.0.2 | -pepquery | -Up-to-date | -- | - | - | - | PepQuery2 peptide-centric MS search for peptide identification and validation | -- | - | Up-to-date | -https://pepquery.org | -Proteomics | -pepquery2 | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 | -
- | peptide_genomic_coordinate | -1.0.0 | -- | python | -To update | -- | - | - | - | Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files | -- | - | To update | -- | Proteomics | -peptide_genomic_coordinate | -galaxyp | -- |
- | peptideshaker | -- | 4.3.6 | -searchgui | -To update | -- | - | - | - | PeptideShaker and SearchGUI | -- | - | To update | -http://compomics.github.io | -Proteomics | -peptideshaker | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker | -
- | pepxml_to_xls | -- | - | - | To update | -- | - | - | - | Convert PepXML to Tabular | -- | - | To update | -- | Proteomics | -pepxml_to_xls | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls | -
- | percolator | -3.5 | -3.5 | -percolator | -Up-to-date | -- | - | - | - | Percolator | -- | - | Up-to-date | -- | Proteomics | -percolator | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator | -
- | pi_db_tools | -1.3 | -- | python | -To update | -- | - | - | - | HiRIEF tools | -- | - | To update | -- | Proteomics | -hirieftools | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools | -
- | pmd_fdr | -1.4.0 | -- | r-base | -To update | -- | - | - | - | Calculate Precursor Mass Discrepancy (PMD) for MS/MS | -- | - | To update | -https://github.com/slhubler/PMD-FDR-for-Galaxy-P | -Proteomics | -pmd_fdr | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr | -
- | custom_pro_db | -1.22.0 | -1.37.1 | -bioconductor-rgalaxy | -To update | -- | - | - | - | CustomProDB | -- | - | To update | -https://bioconductor.org/packages/release/bioc/html/customProDB.html | -Proteomics | -custom_pro_db | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db | -
- | custom_pro_db_annotation_data_manager | -- | - | - | To update | -- | - | - | - | CustomProDB Annotation | -- | - | To update | -https://bioconductor.org/packages/release/bioc/html/customProDB.html | -Proteomics | -custom_pro_db_annotation_data_manager | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db | -
- | psm2sam | -1.3.2.1 | -- | r-base | -To update | -- | - | - | - | PSM to SAM | -- | - | To update | -https://bioconductor.org/packages/release/bioc/html/proBAMr.html | -Proteomics | -psm_to_sam | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam | -
- | proteinpilot | -0.1 | -- | - | To update | -- | - | - | - | - | - | - | To update | -- | - | proteinpilot | -galaxyp | -- |
- | retrieve_ensembl_bed | -0.1.0 | -- | - | To update | -- | - | - | - | Retrieve cDNA features from Ensembl REST API in BED format | -- | - | To update | -http://rest.ensembl.org/ | -Data Source | -retrieve_ensembl_bed | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed | -
- | translate_bed | -0.1.0 | -- | - | To update | -- | - | - | - | Translate BED transcript CDS or cDNA in 3 frames | -- | - | To update | -http://rest.ensembl.org/ | -Proteomics | -translate_bed | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed | -
- | proteomiqon_joinquantpepionswithproteins | -0.0.1 | -0.0.2 | -proteomiqon-joinquantpepionswithproteins | -To update | -- | - | - | - | The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. | -- | - | To update | -https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html | -Proteomics | -proteomiqon_joinquantpepionswithproteins | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins | -
- | proteomiqon_labeledproteinquantification | -0.0.1 | -0.0.3 | -proteomiqon-labeledproteinquantification | -To update | -- | - | - | - | The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. | -- | - | To update | -https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html | -Proteomics | -proteomiqon_labeledproteinquantification | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification | -
- | proteomiqon_labelfreeproteinquantification | -0.0.1 | -0.0.3 | -proteomiqon-labelfreeproteinquantification | -To update | -- | - | - | - | The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. | -- | - | To update | -https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html | -Proteomics | -proteomiqon_labelfreeproteinquantification | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification | -
- | proteomiqon_mzmltomzlite | -0.0.8 | -0.0.8 | -proteomiqon-mzmltomzlite | -Up-to-date | -- | - | - | - | The tool MzMLToMzLite allows to convert mzML files to mzLite files. | -- | - | Up-to-date | -https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html | -Proteomics | -proteomiqon_mzmltomzlite | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite | -
- | proteomiqon_peptidedb | -0.0.7 | -0.0.7 | -proteomiqon-peptidedb | -Up-to-date | -- | - | - | - | The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. | -- | - | Up-to-date | -https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html | -Proteomics | -proteomiqon_peptidedb | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb | -
- | proteomiqon_peptidespectrummatching | -0.0.7 | -0.0.7 | -proteomiqon-peptidespectrummatching | -Up-to-date | -- | - | - | - | Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. | -- | - | Up-to-date | -https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html | -Proteomics | -proteomiqon_peptidespectrummatching | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching | -
- | proteomiqon_proteininference | -0.0.7 | -0.0.7 | -proteomiqon-proteininference | -Up-to-date | -- | - | - | - | MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. | -- | - | Up-to-date | -https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html | -Proteomics | -proteomiqon_proteininference | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference | -
- | proteomiqon_psmbasedquantification | -0.0.8 | -0.0.9 | -proteomiqon-psmbasedquantification | -To update | -- | - | - | - | The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. | -- | - | To update | -https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html | -Proteomics | -proteomiqon_psmbasedquantification | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification | -
- | proteomiqon_psmstatistics | -0.0.8 | -0.0.8 | -proteomiqon-psmstatistics | -Up-to-date | -- | - | - | - | The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. | -- | - | Up-to-date | -https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html | -Proteomics | -proteomiqon_psmstatistics | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics | -
- | proteore_venn_diagram | -2021.06.08 | -- | python | -To update | -- | - | - | - | ProteoRE JVenn Diagram | -- | - | To update | -- | Proteomics | -proteore_venn_diagram | -galaxyp | -- |
- | protxml_to_xls | -0.1.0 | -- | trans_proteomic_pipeline | -To update | -- | - | - | - | - | - | - | To update | -- | - | protxml_to_xls | -galaxyp | -- |
- | psm_eval | -0.1.0 | -- | binaries_for_psm_eval | -To update | -- | - | - | - | - | - | - | To update | -- | - | psm_eval | -galaxyp | -- |
- | psm_validation | -1.0.3 | -- | - | To update | -- | - | - | - | Validate PSM from Ion Fragmentation | -- | - | To update | -https://github.com/galaxyproteomics/psm_fragments.git | -Proteomics | -psm_validation | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation | -
- | pyprophet | -2.1.4 | -2.2.5 | -pyprophet | -To update | -- | - | - | - | Semi-supervised learning and scoring of OpenSWATH results. | -- | - | To update | -https://github.com/PyProphet/pyprophet | -Proteomics | -- | galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet | -
- | pyteomics | -4.4.1 | -4.7.1 | -pyteomics | -To update | -pyteomics | -Pyteomics | -Protein identification | -Proteomics, Proteomics experiment | -Tools using the pyteomics library | -Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. | -- | To update | -https://pyteomics.readthedocs.io/en/latest/ | -Proteomics, Metabolomics | -pyteomics | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics | -
- | quantp | -1.1.2 | -1.11.6 | -r-data.table | -To update | -- | - | - | - | Correlation between protein and transcript abundance | -- | - | To update | -- | Proteomics | -quantp | -galaxyp | -- |
- | quantwiz_iq | -2.0 | -2.0 | -quantwiz-iq | -Up-to-date | -- | - | - | - | Isobaric Quantitation using QuantWiz-IQ | -- | - | Up-to-date | -https://sourceforge.net/projects/quantwiz/ | -Proteomics | -quantwiz_iq | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq | -
- | qupath_roi_splitter | -0.1.0+galaxy1 | -- | geojson | -To update | -- | - | - | - | Split ROI coordinates of QuPath TMA annotation by cell type | -- | - | To update | -https://github.com/npinter/ROIsplitter | -Imaging | -qupath_roi_splitter | -galaxyp | -hhttps://github.com/npinter/ROIsplitter | -
- | rawtools | -- | 2.0.4 | -rawtools | -To update | -- | - | - | - | Raw Tools | -- | - | To update | -https://github.com/kevinkovalchik/RawTools | -Proteomics | -rawtools | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools | -
- | regex_find_replace | -1.0.3 | -- | python | -To update | -- | - | - | - | Use python regular expressions to find and replace text | -- | - | To update | -- | Text Manipulation | -regex_find_replace | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace | -
- | scaffold | -0.1.0 | -- | scaffold | -To update | -- | - | - | - | - | - | - | To update | -- | - | scaffold | -galaxyp | -- |
- | sixgill | -0.2.4 | -0.2.4 | -sixgill | -Up-to-date | -- | - | - | - | Six-frame Genome-Inferred Libraries for LC-MS/MS | -- | - | Up-to-date | -- | Proteomics, MetaProteomics | -sixgill | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill | -
- | spectrast2spectrast_irt | -0.1.0 | -0.11.0 | -msproteomicstools | -To update | -- | - | - | - | Filter from spectraST files to swath input files | -- | - | To update | -- | Proteomics | -spectrast2spectrast_irt | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt | -
- | spectrast2tsv | -0.1.0 | -0.11.0 | -msproteomicstools | -To update | -- | - | - | - | Filter from spectraST files to swath input files | -- | - | To update | -- | Proteomics | -spectrast2tsv | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv | -
- | translate_bed_sequences | -0.2.0 | -1.70 | -biopython | -To update | -- | - | - | - | Perform 3 frame translation of BED file augmented with a sequence column | -- | - | To update | -- | Proteomics | -translate_bed_sequences | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences | -
- | unipept | -4.5.1 | -- | python | -To update | -- | - | - | - | Unipept retrieves metaproteomics information | -- | - | To update | -https://github.com/galaxyproteomics/tools-galaxyp | -Proteomics | -unipept | -galaxyp | -https://unipept.ugent.be/apidocs | -
- | uniprotxml_downloader | -2.4.0 | -- | requests | -To update | -- | - | - | - | Download UniProt proteome in XML or fasta format | -- | - | To update | -- | Proteomics | -uniprotxml_downloader | -galaxyp | -https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader | -
- | validate_fasta_database | -0.1.5 | -1.0 | -validate-fasta-database | -To update | -- | - | - | - | runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. | -- | - | To update | -- | Fasta Manipulation, Proteomics | -validate_fasta_database | -galaxyp | -- |
- | bio3d | -2.4_1 | -2.3_3 | -r-bio3d | -To update | -- | - | - | - | Bio3d is a program that can be used to analyse molecular dynamics trajectories. | -- | - | To update | -http://thegrantlab.org/bio3d/index.php | -Computational chemistry | -bio3d | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d | -
- | biomoldyn | -1.5.2 | -- | scipy | -To update | -- | - | - | - | Tools for MD analysis | -- | - | To update | -https://github.com/moldyn/ | -Molecular Dynamics, Computational chemistry | -biomoldyn | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ | -
- | ambertools | -21.10 | -- | ambertools | -To update | -- | - | - | - | Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. | -- | - | To update | -http://ambermd.org/AmberTools.php | -Molecular Dynamics, Computational chemistry | -ambertools | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ | -
- | packmol | -18.169.1 | -- | packmol | -To update | -- | - | - | - | PACKMOL is a package for creating starting structures for Molecular Dynamics simulations | -- | - | To update | -http://m3g.iqm.unicamp.br/packmol/home.shtml | -Molecular Dynamics, Computational chemistry | -packmol | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem | -
- | topologyeditors | -0 | -- | python | -To update | -- | - | - | - | Set of python scripts and associated tool files that can be used to modify topology files. | -- | - | To update | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors | -Molecular Dynamics, Computational chemistry | -topologyeditors | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors | -
- | free_energy | -- | - | - | To update | -- | - | - | - | Free energy tools of BRIDGE. | -- | - | To update | -- | Molecular Dynamics, Computational chemistry | -freeenergy | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy | -
- | gromacs | -2022 | -2021.3 | -gromacs | -To update | -- | - | - | - | GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. | -- | - | To update | -https://github.com/gromacs | -Molecular Dynamics, Computational chemistry | -gromacs | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs | -
- | mdanalysis | -1.0.0 | -- | mdanalysis | -To update | -- | - | - | - | MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations | -- | - | To update | -https://github.com/MDAnalysis/mdanalysis | -Computational chemistry | -mdanalysis | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ | -
- | mdfileconverter | -1.9.7 | -- | mdtraj | -To update | -- | - | - | - | A tool for interconverting between different MD structure and trajectory file formats. | -- | - | To update | -- | Molecular Dynamics, Computational chemistry | -md_converter | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter | -
- | mdslicer | -1.9.9 | -- | mdtraj | -To update | -- | - | - | - | A tool for slicing trajectory files using MDTraj. | -- | - | To update | -- | Molecular Dynamics, Computational chemistry | -md_converter | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer | -
- | mdtraj | -1.9.7 | -- | mdtraj | -To update | -- | - | - | - | MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories | -- | - | To update | -https://github.com/mdtraj/mdtraj | -Computational chemistry | -mdtraj | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ | -
- | openmm | -1.8.1 | -- | pdbfixer | -To update | -- | - | - | - | OpenMM is a toolkit for molecular simulation using high performance GPU code. | -- | - | To update | -https://github.com/openmm | -Molecular Dynamics, Computational chemistry | -openmm | -chemteam | -https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm | -
- | vmd | -- | - | - | To update | -- | - | - | - | vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations | -- | - | To update | -https://www.ks.uiuc.edu/Research/vmd/ | -Computational chemistry | -vmd | -chemteam | -https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd | -
- | artbio_bam_cleaning | -1.10+galaxy0 | -1.19.2 | -samtools | -To update | -- | - | - | - | filter bam files before somatic-varscan or lumpy-smoove analysis | -- | - | To update | -http://artbio.fr | -SAM, Variant Analysis | -artbio_bam_cleaning | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning | -
- | bamparse | -4.1.1 | -0.22.0 | -pysam | -To update | -- | - | - | - | Generates hit count lists from bam alignments. | -- | - | To update | -http://artbio.fr | -RNA, Transcriptomics | -bamparse | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse | -
- | bigwig_to_bedgraph | -377+galaxy1 | -448 | -ucsc-bigwigtobedgraph | -To update | -- | - | - | - | Converts a bigWig file to bedGraph format | -- | - | To update | -http://artbio.fr | -Convert Formats | -bigwig_to_bedgraph | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph | -
- | bigwig_to_wig | -3+galaxy0 | -377 | -ucsc-bigwiginfo | -To update | -- | - | - | - | Converts a bigWig file to Wiggle (WIG) format | -- | - | To update | -https://artbio.fr | -Convert Formats | -bigwig_to_wig | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig | -
- | blast_to_scaffold | -1.1.0 | -- | python | -To update | -- | - | - | - | Generate DNA scaffold from blastn or tblastx alignments of Contigs | -- | - | To update | -http://artbio.fr | -RNA, Sequence Analysis, Assembly | -blast_to_scaffold | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold | -
- | blast_unmatched | -1.0.1 | -- | python | -To update | -- | - | - | - | Extract unmatched query sequences from blast | -- | - | To update | -http://artbio.fr | -Fasta Manipulation | -blast_unmatched | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched | -
- | blastparser_and_hits | -2.7.1 | -- | python | -To update | -- | - | - | - | Parse blast outputs and compile hits | -- | - | To update | -http://artbio.fr | -Assembly, RNA | -blastparser_and_hits | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits | -
- | blastx_to_scaffold | -1.1.1 | -- | python | -To update | -- | - | - | - | Generate DNA scaffold from blastx alignment of Contigs | -- | - | To update | -http://artbio.fr | -RNA, Sequence Analysis, Assembly | -blastx_to_scaffold | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold | -
- | cap3 | -2.0.1 | -10.2011 | -cap3 | -To update | -- | - | - | - | cap3 wrapper | -- | - | To update | -http://artbio.fr | -Assembly | -cap3 | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 | -
- | cherry_pick_fasta | -4.1 | -- | python | -To update | -- | - | - | - | Pick fasta sequence with specific header content | -- | - | To update | -http://artbio.fr | -Fasta Manipulation | -cherry_pick_fasta | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta | -
- | concat_multi_datasets | -1.4.2 | -- | - | To update | -- | - | - | - | Concatenate multiple datasets tail-to-head, including collection datasets. | -- | - | To update | -http://artbio.fr | -Text Manipulation | -concatenate_multiple_datasets | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets | -
- | cpm_tpm_rpk | -0.5.2 | -1.3.2 | -r-optparse | -To update | -- | - | - | - | Generate CPM,TPM or RPK from raw counts | -- | - | To update | -http://artbio.fr | -Transcriptomics | -cpm_tpm_rpk | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk | -
- | deseq2_normalization | -1.40.2+galaxy0 | -1.42.0 | -bioconductor-deseq2 | -To update | -- | - | - | - | Normalizes gene hitlists | -- | - | To update | -http://artbio.fr | -RNA, Transcriptomics, Sequence Analysis, Statistics | -deseq2_normalization | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization | -
- | embl2fa | -0.2 | -- | - | To update | -- | - | - | - | Converts EMBL flat format to fasta format | -- | - | To update | -http://artbio.fr | -Text Manipulation | -embl2fa | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa | -
- | ez_histograms | -3.4.4 | -2.2.1 | -r-ggplot2 | -To update | -- | - | - | - | ggplot2 histograms and density plots | -- | - | To update | -https://github.com/tidyverse/ggplot2 | -Visualization, Statistics | -ez_histograms | -artbio | -https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms | -
- | fetch_fasta_from_ncbi | -3.1.0 | -1.12 | -urllib3 | -To update | -- | - | - | - | Fetch fasta sequences from NCBI using eutils wrappers | -- | - | To update | -http://artbio.fr | -Fasta Manipulation, Data Source | -fetch_fasta_from_ncbi | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi | -
- | fisher_test | -2.32.0+galaxy0 | -2.34.0 | -bioconductor-qvalue | -To update | -- | - | - | - | Fisher's exact test on two-column hit lists. | -- | - | To update | -http://artbio.fr | -RNA, Statistics | -fishertest | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test | -
- | gatk4 | -4.1.7.0 | -4.5.0.0 | -gatk4 | -To update | -- | - | - | - | Find somatic variations | -- | - | To update | -http://artbio.fr | -Variant Analysis | -gatk4 | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 | -
- | get_reference_fasta | -0.3.2 | -- | - | To update | -- | - | - | - | Obtain reference genome sequence. | -- | - | To update | -http://artbio.fr | -Data Source, Fasta Manipulation | -get_reference_fasta | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta | -
- | gsc_center_scale | -4.3.1+galaxy0 | -1.3.2 | -r-optparse | -To update | -- | - | - | - | Center or scale (standardize) data | -- | - | To update | -http://artbio.fr | -Statistics | -gsc_center_scale | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale | -
- | gsc_filter_cells | -4.3.1+galaxy0 | -1.3.2 | -r-optparse | -To update | -- | - | - | - | Filter single cell RNAseq data on libray depth and number of detected genes | -- | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_filter_cells | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells | -
- | gsc_filter_genes | -4.3.1+galaxy0 | -1.3.2 | -r-optparse | -To update | -- | - | - | - | Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data | -- | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_filter_genes | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes | -
- | gsc_gene_expression_correlations | -4.3.1+galaxy0 | -1.3.2 | -r-optparse | -To update | -- | - | - | - | Compute single-cell paire-wise gene expressions correlations | -- | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_gene_expression_correlations | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations | -
- | gsc_high_dimensions_visualisation | -4.3+galaxy0 | -1.3.2 | -r-optparse | -To update | -- | - | - | - | Generates PCA, t-SNE and HCPC visualisation | -- | - | To update | -http://artbio.fr | -Transcriptomics, Visualization | -gsc_high_dimensions_visualisation | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization | -
- | gsc_mannwhitney_de | -4.1.3+galaxy0 | -1.3.2 | -r-optparse | -To update | -- | - | - | - | Perform a mann-whitney differential testing between two sets of gene expression data | -- | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_mannwhitney_de | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de | -
- | gsc_scran_normalize | -1.28.1+galaxy0 | -1.30.0 | -bioconductor-scran | -To update | -- | - | - | - | Normalize raw counts using scran | -- | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_scran_normalize | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize | -
- | gsc_signature_score | -2.3.9+galaxy0 | -1.3.2 | -r-optparse | -To update | -- | - | - | - | Compute signature scores from single cell RNAseq data | -- | - | To update | -http://artbio.fr | -Transcriptomics | -gsc_signature_score | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score | -
- | guppy | -0.2.2 | -- | - | To update | -- | - | - | - | A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies | -- | - | To update | -http://artbio.fr | -Nanopore | -guppy_basecaller | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy | -
- | high_dim_heatmap | -3.1.3+galaxy0 | -2.17.0 | -r-gplots | -To update | -- | - | - | - | gplot heatmap.2 function adapted for plotting large heatmaps | -- | - | To update | -https://github.com/cran/gplots | -Visualization | -high_dim_heatmap | -artbio | -https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap | -
- | justdiff | -3.10+galaxy0 | -- | diffutils | -To update | -- | - | - | - | Unix diff | -- | - | To update | -http://artbio.fr | -Text Manipulation | -justdiff | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff | -
- | justgzip | -2.8+galaxy0 | -- | pigz | -To update | -- | - | - | - | Compress fastq sequence files | -- | - | To update | -http://artbio.fr | -Convert Formats | -justgzip | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip | -
- | lumpy_smoove | -0.2.8+galaxy1 | -0.7.1 | -svtyper | -To update | -- | - | - | - | Galaxy wrapper of the lumpy-using smoove workflow | -- | - | To update | -http://artbio.fr | -Variant Analysis | -lumpy_smoove | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove | -
- | manta | -1.6 | -1.6.0 | -manta | -To update | -- | - | - | - | Structural variant and indel caller for mapped sequencing data | -- | - | To update | -http://artbio.fr | -Variant Analysis | -manta | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/manta | -
- | mapping_quality_stats | -0.22.0 | -1.3.2 | -r-optparse | -To update | -- | - | - | - | Collects and shows the distribution of MAPQ values in a BAM alignment file | -- | - | To update | -http://artbio.fr | -Sequence Analysis, Statistics | -mapping_quality_stats | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats | -
- | mircounts | -1.6 | -- | tar | -To update | -- | - | - | - | Generates miRNA count lists from read alignments to mirBase. | -- | - | To update | -http://artbio.fr | -RNA, Transcriptomics | -mircounts | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts | -
- | mutational_patterns | -3.12.0 | -3.12.0 | -bioconductor-mutationalpatterns | -Up-to-date | -- | - | - | - | Mutational patterns and signatures in base substitution catalogs | -- | - | Up-to-date | -http://artbio.fr | -Variant Analysis | -mutational_patterns | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns | -
- | oases | -1.4.0 | -0.2.09 | -oases | -To update | -- | - | - | - | Short read assembler | -- | - | To update | -http://artbio.fr | -Assembly, RNA | -oases | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/oases | -
- | pathifier | -1.40.0 | -1.40.0 | -bioconductor-pathifier | -Up-to-date | -- | - | - | - | pathifier | -- | - | Up-to-date | -https:// | -Transcriptomics, Statistics | -pathifier | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier | -
- | pindel | -0.2.5b9 | -0.2.5b9 | -pindel | -Up-to-date | -- | - | - | - | Pindel detects genome-wide structural variation. | -- | - | Up-to-date | -http://artbio.fr | -Variant Analysis | -pindel | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel | -
- | probecoverage | -0.22.0 | -0.22.0 | -pysam | -Up-to-date | -- | - | - | - | computes and plots read coverage of genomic regions by sequencing datasets | -- | - | Up-to-date | -http://artbio.fr | -Sequence Analysis, Genomic Interval Operations, Graphics, Statistics | -probecoverage | -artbio | -https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage | -
- | repenrich | -1.5.2 | -4.0.2 | -bioconductor-edger | -To update | -- | - | - | - | Repeat element profiling | -- | - | To update | -https://github.com/nskvir/RepEnrich | -Transcriptomics, Variant Analysis | -repenrich | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich | -
- | rsem | -- | 1.3.3 | -rsem | -To update | -- | - | - | - | transcript quantification from RNA-Seq data | -- | - | To update | -https://github.com/deweylab/RSEM | -Transcriptomics, RNA | -rsem | -artbio | -https://github.com/artbio/tools-artbio/tree/master/tools/rsem | -
- | sambamba | -0.7.1+galaxy1 | -1.0 | -sambamba | -To update | -- | - | - | - | filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM | -- | - | To update | -http://artbio.fr | -SAM | -sambamba | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba | -
- | sashimi_plot | -0.1.1 | -- | python | -To update | -- | - | - | - | Generates a sashimi plot from bam files. | -- | - | To update | -http://artbio.fr | -RNA, Transcriptomics, Graphics, Visualization | -sashimi_plot | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot | -
- | sequence_format_converter | -2.2.0 | -- | python | -To update | -- | - | - | - | various fasta to tabular conversions | -- | - | To update | -http://artbio.fr | -Convert Formats, Fasta Manipulation | -sequence_format_converter | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter | -
- | small_rna_clusters | -1.3.0 | -0.22.0 | -pysam | -To update | -- | - | - | - | clusters small rna reads in alignment BAM files | -- | - | To update | -http://artbio.fr | -RNA, SAM, Graphics, Next Gen Mappers | -small_rna_clusters | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters | -
- | small_rna_maps | -3.1.1 | -- | numpy | -To update | -- | - | - | - | Generates small read maps from alignment BAM files | -- | - | To update | -http://artbio.fr | -RNA, SAM, Graphics, Next Gen Mappers | -small_rna_maps | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps | -
- | small_rna_signatures | -3.4.2 | -0.22.0 | -pysam | -To update | -- | - | - | - | Computes the tendency of small RNAs to overlap with each other. | -- | - | To update | -http://artbio.fr | -RNA | -small_rna_signatures | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures | -
- | snvtocnv | -3.0.0+galaxy1 | -3.0.0 | -sequenza-utils | -To update | -- | - | - | - | infer copy number variations from a vcf file with SNVs using R sequenza | -- | - | To update | -http://artbio.fr | -Variant Analysis | -snvtocnv | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv | -
- | sr_bowtie | -2.3.0 | -1.3.1 | -bowtie | -To update | -- | - | - | - | bowtie wrapper tool to align small RNA sequencing reads | -- | - | To update | -http://artbio.fr | -RNA, Next Gen Mappers | -sr_bowtie | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie | -
- | sr_bowtie_dataset_annotation | -2.8 | -1.3.1 | -bowtie | -To update | -- | - | - | - | Maps iteratively small RNA sequencing datasets to reference sequences. | -- | - | To update | -http://artbio.fr | -RNA | -sr_bowtie_dataset_annotation | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation | -
- | tarfast5 | -0.6.1 | -- | pigz | -To update | -- | - | - | - | produces a tar.gz archive of fast5 sequence files | -- | - | To update | -http://artbio.fr | -Nanopore | -tarfast5 | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 | -
- | varscan_vaf | -0.1 | -- | python | -To update | -- | - | - | - | Compute variant allele frequency in vcf files generated by varscan. | -- | - | To update | -http://artbio.fr | -Variant Analysis | -varscan_vaf | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf | -
- | xpore | -2.1+galaxy0 | -2.1 | -xpore | -To update | -- | - | - | - | Identification and quantification of differential RNA modifications from direct RNA sequencing | -- | - | To update | -https://github.com/GoekeLab/xpore | -Nanopore | -xpore | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore | -
- | yac_clipper | -2.5.1 | -- | python | -To update | -- | - | - | - | Clips 3' adapters for small RNA sequencing reads. | -- | - | To update | -http://artbio.fr | -RNA, Fastq Manipulation | -yac_clipper | -artbio | -https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper | -
- | EMLassemblyline | -0.1.1+galaxy0 | -- | r-emlassemblyline | -To update | -- | - | - | - | Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa | -- | - | To update | -https://github.com/EDIorg/EMLassemblyline | -Ecology | -emlassemblyline | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline | -
- | Ecoregionalization_workflow | -0.1.0+galaxy0 | -- | r-base | -To update | -- | - | - | - | Tools to compute ecoregionalization with BRT model predictions and clustering. | -- | - | To update | -https://github.com/PaulineSGN/Workflow_Galaxy | -Ecology | -ecoregionalization | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow | -
- | Geom_mean_workflow | -0.1.0+galaxy0 | -- | r-base | -To update | -- | - | - | - | Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). | -- | - | To update | -https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom | -Ecology | -Geometric means (Dead wood) | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow | -
- | PAMPA | -0.0.2 | -- | - | To update | -- | - | - | - | Tools to compute and analyse biodiversity metrics | -- | - | To update | -- | Ecology | -pampa | -ecology | -https://github.com/ColineRoyaux/PAMPA-Galaxy | -
- | ab1_fastq | -1.20.0 | -1.38.0 | -bioconductor-sangerseqr | -To update | -- | - | - | - | Tool to convert ab1 files into FASTQ files | -- | - | To update | -- | Convert Formats | -ab1fastq | -ecology | -https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq | -
- | champ_blocs | -0.0.0 | -- | r-base | -To update | -- | - | - | - | Compute indicators for turnover boulders fields | -- | - | To update | -- | Ecology | -- | ecology | -https://github.com/Marie59/champ_blocs | -
- | consensus_from_alignments | -1.0.0 | -- | r-bioseq | -To update | -- | - | - | - | Tool to compute a consensus sequence from several aligned fasta sequences | -- | - | To update | -- | Sequence Analysis | -consalign | -ecology | -https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments | -
- | data_exploration | -0.0.0 | -- | r-tangles | -To update | -- | - | - | - | Explore data through multiple statistical tools | -- | - | To update | -- | Ecology | -- | ecology | -https://github.com/Marie59/Data_explo_tools | -
- | xarray | -2022.3.0 | -- | xarray | -To update | -- | - | - | - | xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. | -- | - | To update | -http://xarray.pydata.org | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ | -
- | gdal | -3.0.0 | -- | - | To update | -- | - | - | - | Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. | -- | - | To update | -https://www.gdal.org | -Ecology | -gdal | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal | -
- | interpolation | -1.0 | -- | r-getopt | -To update | -- | - | - | - | Run IDW interpolation based on a .csv and .geojson file | -- | - | To update | -https://github.com/AquaINFRA/galaxy | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation | -
- | medenv | -0.0.1 | -- | pandas | -To update | -- | - | - | - | Retrieve environmental data from etopo, cmems and woa | -- | - | To update | -https://github.com/jeremyfix/medenv | -Ecology, Data Source | -- | ecology | -https://github.com/jeremyfix/medenv | -
- | obisindicators | -0.0.2 | -- | r-base | -To update | -- | - | - | - | Compute biodiveristy indicators for marine data from obis | -- | - | To update | -https://github.com/Marie59/obisindicators | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators | -
- | ocean | -0.1.15 | -- | - | To update | -- | - | - | - | Access, process, visualise oceanographic data for the Earth System | -- | - | To update | -https://github.com/Marie59/FE-ft-ESG/tree/main/argo | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean | -
- | regionalgam | -1.5 | -- | r-mgcv | -To update | -- | - | - | - | - | - | - | To update | -https://github.com/RetoSchmucki/regionalGAM | -Ecology | -- | ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam | -
- | spocc | -1.2.2 | -- | - | To update | -- | - | - | - | Get species occurences data | -- | - | To update | -https://cran.r-project.org/web/packages/spocc/index.html | -Ecology | -spocc_occ | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc | -
- | srs_tools | -0.0.1 | -- | r-base | -To update | -- | - | - | - | Compute biodiversity indicators for remote sensing data from Sentinel 2 | -- | - | To update | -- | Ecology | -- | ecology | -https://github.com/Marie59/Sentinel_2A/srs_tools | -
- | stoc | -0.0.2 | -- | - | To update | -- | - | - | - | Tools to analyse STOC data. | -- | - | To update | -- | Ecology | -stoceps | -ecology | -https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc | -
- | vigiechiro | -0.1.1 | -- | - | To update | -- | - | - | - | Tools created by the vigiechiro team to analyses and identify chiro sounds files. | -- | - | To update | -https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro | -Ecology | -vigiechiro | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro | -
- | xmlstarlet | -1.6.1 | -- | xmlstarlet | -To update | -- | - | - | - | Tool to convert a xml file from one metadata standard to another | -- | - | To update | -- | Convert Formats | -xmlstarlet | -ecology | -https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet | -
- | c3s | -0.2.0 | -- | python | -To update | -- | - | - | - | Copernicus Climate Change Service (C3S) | -- | - | To update | -https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset | -Climate Analysis | -c3s | -climate | -https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s | -
- | cads | -0.1.0 | -- | python | -To update | -- | - | - | - | Copernicus Atmosphere Data Store (ADS) | -- | - | To update | -https://ads.atmosphere.copernicus.eu/#!/home | -Climate Analysis | -cads | -climate | -https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads | -
- | cdo | -2.0.0 | -- | - | To update | -- | - | - | - | CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. | -- | - | To update | -https://code.mpimet.mpg.de/projects/cdo/ | -Climate Analysis | -- | climate | -https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo | -
- | cesm | -2.1.3 | -2.1.3 | -cesm | -Up-to-date | -- | - | - | - | Community Earth System Model (CESM) | -- | - | Up-to-date | -https://www.cesm.ucar.edu/ | -Climate Analysis | -cesm | -climate | -https://github.com/ESCOMP/CESM | -
- | climate-stripes | -1.0.2 | -- | python | -To update | -- | - | - | - | Create climate stripes from a tabular input file | -- | - | To update | -https://www.climate-lab-book.ac.uk/2018/warming-stripes/ | -Climate Analysis, Visualization | -climate_stripes | -climate | -https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes | -
- | eodie | -1.0.2 | -- | eodie | -To update | -- | - | - | - | Earth Observation Data Information Extractor | -- | - | To update | -https://eodie.readthedocs.io/ | -Climate Analysis | -eodie | -climate | -https://gitlab.com/eetun-tiimi/EODIE | -
- | essential_climate_variables | -0.2.0 | -- | python | -To update | -- | - | - | - | Get Copernicus Essential Climate Variables for assessing climate variability | -- | - | To update | -https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview | -Climate Analysis, Data Source | -cds_essential_variability | -climate | -https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables | -
- | fates-emerald | -2.0 | -- | fates-emerald | -To update | -- | - | - | - | EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model | -- | - | To update | -https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api | -Climate Analysis | -ctsm_fates | -climate | -https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald | -
- | mean-per-zone | -0.2.0 | -- | python | -To update | -- | - | - | - | Creates a png image showing statistic over areas as defined in the vector file | -- | - | To update | -https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ | -Visualization, GIS, Climate Analysis | -mean_per_zone | -climate | -https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone | -
- | psy-maps | -1.2.1 | -- | python | -To update | -- | - | - | - | Visualization of regular geographical data on a map with psyplot | -- | - | To update | -https://github.com/Chilipp/psy-maps | -Visualization, Climate Analysis | -psy_maps | -climate | -https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps | -
- | shift-longitudes | -0.1.0 | -- | python | -To update | -- | - | - | - | Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees | -- | - | To update | -https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ | -Climate Analysis | -shift_longitudes | -climate | -https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes | -
- | smithsonian-volcanoes | -0.1.0 | -- | python | -To update | -- | - | - | - | Retrieve data from Volcanoes of the World (VOTW) Database | -- | - | To update | -https://volcano.si.edu/gvp_votw.cfm | -Retrieve Data | -smithsonian_volcanoes | -climate | -https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes | -
- | droplet-barcode-plot | -1.6.1+galaxy2 | -0.0.1 | -scxa-plots | -To update | -- | - | - | - | Make a cell barcode plot for droplet single-cell RNA-seq QC | -- | - | To update | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary | -Sequence Analysis | -droplet_barcode_plot | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml | -
- | fastq_provider | -0.4.4 | -0.4.7 | -atlas-fastq-provider | -To update | -- | - | - | - | Retrieval and download of FASTQ files from ENA and other repositories such as HCA. | -- | - | To update | -https://github.com/ebi-gene-expression-group/atlas-fastq-provider | -Data Source, RNA, Transcriptomics | -atlas_fastq_provider | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider | -
- | gtf-2-gene-list | -1.52.0+galaxy0 | -1.1.0 | -atlas-gene-annotation-manipulation | -To update | -- | - | - | - | Utility to extract annotations from Ensembl GTF files. | -- | - | To update | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary | -Sequence Analysis | -gtf2gene_list | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml | -
- | fastq_pair | -1.0+galaxy0 | -1.0 | -fastq-pair | -To update | -- | - | - | - | Paired-end fastq pairer | -- | - | To update | -https://github.com/linsalrob/fastq-pair | -Fastq Manipulation | -fastq_pair | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair | -
- | fastq_quality_trimmer | -0.0.14+galaxy0 | -0.0.14 | -fastx_toolkit | -To update | -- | - | - | - | FASTQ trimmer based on quality | -- | - | To update | -https://github.com/agordon/fastx_toolkit | -Fastq Manipulation | -fastq_quality_trimmer | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer | -
- | fastq_utils | -0.25.1+galaxy0 | -0.25.2 | -fastq_utils | -To update | -- | - | - | - | Set of tools for handling fastq files | -- | - | To update | -https://github.com/nunofonseca/fastq_utils | -Transcriptomics, RNA | -fastq_utils | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils | -
- | salmon-kallisto-mtx-to-10x | -0.0.1+galaxy6 | -- | scipy | -To update | -- | - | - | - | Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data | -- | - | To update | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary | -Sequence Analysis | -salmon_kallisto_mtx_to_10x | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml | -
- | cell-types-analysis | -1.1.1 | -0.1.11 | -cell-types-analysis | -To update | -- | - | - | - | Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis | -- | - | To update | -- | Transcriptomics, RNA, Statistics | -suite_cell_types_analysis | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | data-hca | -v0.0.4+galaxy0 | -0.0.4 | -hca-matrix-downloader | -To update | -- | - | - | - | Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects | -- | - | To update | -- | Transcriptomics, Sequence Analysis | -suite_human_cell_atlas_tools | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | data-scxa | -v0.0.2+galaxy2 | -- | wget | -To update | -- | - | - | - | Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home | -- | - | To update | -- | Transcriptomics, Sequence Analysis | -suite_ebi_expression_atlas | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | decoupler | -1.4.0+galaxy1 | -1.5.0 | -decoupler | -To update | -- | - | - | - | decoupler - Ensemble of methods to infer biological activities | -- | - | To update | -https://decoupler-py.readthedocs.io/en/latest/ | -Transcriptomics | -suite_decoupler | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | dropletutils | -1.0.4 | -0.0.5 | -dropletutils-scripts | -To update | -- | - | - | - | De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 | -- | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_dropletutils | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | garnett | -0.2.8 | -0.0.5 | -garnett-cli | -To update | -- | - | - | - | De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 | -- | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_garnett | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | monocle3 | -0.1.4 | -0.0.9 | -monocle3-cli | -To update | -- | - | - | - | De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. | -- | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_monocle3 | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | sc3 | -1.8.0 | -0.0.6 | -sc3-scripts | -To update | -- | - | - | - | De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. | -- | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_sc3 | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | scanpy | -1.9.3 | -1.9.301 | -scanpy-scripts | -To update | -- | - | - | - | scanpy-scripts, command-line wrapper scripts around Scanpy. | -- | - | To update | -https://scanpy.readthedocs.io | -Transcriptomics, Sequence Analysis, RNA | -scanpy_scripts | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy | -
- | scater | -1.10.0 | -0.0.5 | -scater-scripts | -To update | -- | - | - | - | De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. | -- | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_scater | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | sccaf | -0.0.9 | -0.0.10 | -sccaf | -To update | -- | - | - | - | SCCAF: Single Cell Clustering Assessment Framework. | -- | - | To update | -https://github.com/sccaf/sccaf | -Transcriptomics | -SCCAF | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf | -
- | sceasy | -0.0.5 | -0.0.7 | -r-sceasy | -To update | -- | - | - | - | Convert scRNA data object between popular formats | -- | - | To update | -- | Transcriptomics | -sceasy | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | scmap | -1.6.3 | -0.1.0 | -scmap-cli | -To update | -- | - | - | - | De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. | -- | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_scmap | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | scpred | -1.0.2 | -0.1.0 | -scpred-cli | -To update | -- | - | - | - | De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 | -- | - | To update | -- | Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_scpred | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -
- | seurat | -4.0.0 | -4.0.0 | -seurat-scripts | -Up-to-date | -- | - | - | - | De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 | -- | - | Up-to-date | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ | -Transcriptomics, RNA, Statistics, Sequence Analysis | -suite_seurat | -ebi-gxa | -- |
- | ucsc-cell-browser | -1.0.0+galaxy1 | -1.2.5 | -ucsc-cell-browser | -To update | -- | - | - | - | Python pipeline and Javascript scatter plot library for single-cell datasets | -- | - | To update | -https://cells.ucsc.edu/ | -Transcriptomics | -ucsc_cell_browser | -ebi-gxa | -https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml | -
- | biotransformer | -3.0.20230403 | -3.0.20230403 | -biotransformer | -Up-to-date | -biotransformer | -BioTransformer | -Metabolic pathway prediction, PTM site prediction, Natural product identification | -Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR | -BioTransformer is a tool for prediction of small molecule metabolism in mammals. | -BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. | -- | Up-to-date | -https://bitbucket.org/djoumbou/biotransformerjar/src/master/ | -Metabolomics | -biotransformer | -recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer | -
- | filter_compounds | -3.1.1 | -2.3.90dev7d621d9 | -openbabel | -To update | -- | - | - | - | Tool for filtering organometallics/anorganic compounds from a list of compounds. | -- | - | To update | -https://github.com/RECETOX/galaxytools/ | -Metabolomics | -filter_compounds | -recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds | -
- | matchms | -0.24.0 | -0.24.2 | -matchms | -To update | -matchms | -Matchms | -Spectral library search, Format validation, Filtering | -Metabolomics | -Searching, filtering and converting mass spectral libraries. | -Tool to import, process, clean, and compare mass spectrometry data. | -- | To update | -https://github.com/matchms/matchms | -Metabolomics | -matchms | -recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/matchms | -
- | misc | -1.0.0 | -- | - | To update | -- | - | - | - | - | - | - | To update | -https://github.com/RECETOX/galaxytools | -Metabolomics | -- | recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/misc | -
- | msmetaenhancer | -0.3.0 | -0.3.0 | -msmetaenhancer | -Up-to-date | -msmetaenhancer | -MSMetaEnhancer | -Annotation, Standardisation and normalisation | -Metabolomics, Compound libraries and screening, Data submission, annotation and curation | -- | Tool for mass spectra metadata annotation. | -- | Up-to-date | -https://github.com/RECETOX/MSMetaEnhancer | -Metabolomics | -- | recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer | -
- | msp_merge | -0.1.0 | -0.24.2 | -matchms | -To update | -- | - | - | - | - | - | - | To update | -https://github.com/RECETOX/galaxytools | -Metabolomics | -- | recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge | -
- | mzml_validator | -0.1.0+galaxy2 | -- | lxml | -To update | -- | - | - | - | mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. | -- | - | To update | -https://github.com/RECETOX/galaxytools | -Metabolomics, Proteomics | -- | recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator | -
- | qcxms | -5.2.1 | -- | - | To update | -- | - | - | - | QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). | -- | - | To update | -https://github.com/grimme-lab/QCxMS | -Computational chemistry, Molecular Dynamics | -QCxMS | -recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms | -
- | query | -0.2 | -- | click | -To update | -- | - | - | - | Execute an SQL statement on a set of tables | -- | - | To update | -- | Text Manipulation | -query | -recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/query | -
- | ramclustr | -1.3.0 | -1.3.1 | -r-ramclustr | -To update | -ramclustr | -RAMClustR | -Imputation, Standardisation and normalisation, Clustering, Correlation | -Metabolomics | -- | A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. | -- | To update | -https://rdrr.io/cran/RAMClustR/ | -Metabolomics | -- | recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr | -
- | recetox_aplcms | -0.12.0 | -0.12.0 | -r-recetox-aplcms | -Up-to-date | -recetox-aplcms | -recetox-aplcms | -Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment | -Metabolomics | -Peak detection tool for HRMS profile data. | -recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. | -- | Up-to-date | -https://github.com/RECETOX/recetox-aplcms | -Metabolomics | -recetox-aplcms | -recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms | -
- | recetox_msfinder | -v3.5.2 | -- | - | To update | -recetox-msfinder | -recetox-msfinder | -Annotation | -Metabolomics | -- | This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. | -- | To update | -https://github.com/RECETOX/recetox-msfinder | -Metabolomics | -- | recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder | -
- | recetox_xmsannotator | -0.10.0 | -0.10.0 | -r-recetox-xmsannotator | -Up-to-date | -recetox-xmsannotator | -recetox-xMSannotator | -Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation | -- | - | Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. | -- | Up-to-date | -https://github.com/RECETOX/recetox-xMSannotator | -Metabolomics | -- | recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator | -
- | rem_complex | -1.0.0 | -- | pandas | -To update | -- | - | - | - | Removes molecular coordination complexes. | -- | - | To update | -https://github.com/RECETOX/galaxytools | -Metabolomics | -rem_complex | -recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex | -
- | retip | -0.5.4 | -- | - | To update | -retip | -Retip | -Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition | -Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry | -- | Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. | -- | To update | -https://github.com/PaoloBnn/Retip | -Metabolomics | -- | recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/retip | -
- | riassigner | -0.4.0 | -0.4.0 | -riassigner | -Up-to-date | -riassigner | -RIAssigner | -Standardisation and normalisation | -Metabolomics, Compound libraries and screening, Data submission, annotation and curation | -- | RIAssigner is a python tool for retention index (RI) computation for GC-MS data. | -- | Up-to-date | -https://github.com/RECETOX/RIAssigner | -Metabolomics | -- | recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner | -
- | rmassbank | -3.0.0 | -- | python | -To update | -- | - | - | - | RMassBank is an R package for processing tandem MS files and building of MassBank records. | -- | - | To update | -https://github.com/MassBank/RMassBank | -Metabolomics | -rmassbank | -recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank | -
- | spec2vec | -0.8.0 | -0.8.0 | -spec2vec | -Up-to-date | -spec2vec | -Spec2Vec | -Spectrum calculation, Spectral library search, Database search, Natural product identification | -Proteomics experiment, Metabolomics, Natural language processing, Proteomics | -Mass spectra similarity scoring using a trained Spec2Vec model. | -Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. | -- | Up-to-date | -https://github.com/iomega/spec2vec | -Metabolomics | -spec2vec | -recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec | -
- | waveica | -0.2.0 | -0.2.0 | -r-recetox-waveica | -Up-to-date | -waveica | -WaveICA | -Standardisation and normalisation | -Metabolomics | -Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. | -Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. | -- | Up-to-date | -https://github.com/RECETOX/WaveICA | -Metabolomics | -- | recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/waveica | -
- | xtb | -6.6.1 | -- | xtb | -To update | -- | - | - | - | Performs semiempirical molecular optimization. | -- | - | To update | -https://github.com/grimme-lab/xtb | -Metabolomics | -xtb_molecular_optimization | -recetox | -https://github.com/RECETOX/galaxytools/tree/master/tools/xtb | -
- | consolidate_vcfs | -1.8.2 | -1.8.2 | -snvphyl-tools | -Up-to-date | -- | - | - | - | Combines freebayes and mpileup files for use by vcf2snvalignment | -- | - | Up-to-date | -https://snvphyl.readthedocs.io/en/latest/ | -Sequence Analysis | -consolidate_vcfs | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | filter_density | -1.8.2 | -1.8.2 | -snvphyl-tools | -Up-to-date | -- | - | - | - | Filter out position based on distance between SNVs | -- | - | Up-to-date | -https://snvphyl.readthedocs.io/en/latest/ | -Sequence Analysis | -filter_density | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | filter_stats | -1.8.2 | -1.8.2 | -snvphyl-tools | -Up-to-date | -- | - | - | - | SNVPhyl filter_stats | -- | - | Up-to-date | -https://snvphyl.readthedocs.io/en/latest/ | -Sequence Analysis | -filter_stats | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | filter_vcf | -1.8.2 | -1.8.2 | -snvphyl-tools | -Up-to-date | -- | - | - | - | SNVPhyl filter_vcf | -- | - | Up-to-date | -https://snvphyl.readthedocs.io/en/latest/ | -Sequence Analysis | -filter_vcf | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | find_repeats | -1.8.2 | -1.8.2 | -snvphyl-tools | -Up-to-date | -- | - | - | - | Find repetitive regions on a reference genome using MUMMer | -- | - | Up-to-date | -https://snvphyl.readthedocs.io/en/latest/ | -Sequence Analysis | -find_repeats | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | positions2snv_alignment | -1.8.2 | -1.8.2 | -snvphyl-tools | -Up-to-date | -- | - | - | - | Generate alignment of SNVs from SNVPhyl variant table. | -- | - | Up-to-date | -https://snvphyl.readthedocs.io/en/latest/ | -Variant Analysis | -positions2snv_alignment | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | positions2snv_invariant_alignment | -1.8.2 | -1.8.2 | -snvphyl-tools | -Up-to-date | -- | - | - | - | Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. | -- | - | Up-to-date | -https://snvphyl.readthedocs.io/en/latest/ | -Variant Analysis | -positions2snv_invariant_alignment | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | snv_matrix | -1.8.2 | -1.8.2 | -snvphyl-tools | -Up-to-date | -- | - | - | - | Generate matrix of SNV distances | -- | - | Up-to-date | -https://snvphyl.readthedocs.io/en/latest/ | -Sequence Analysis | -snv_matrix | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | vcf2snvalignment | -1.8.2 | -1.8.2 | -snvphyl-tools | -Up-to-date | -- | - | - | - | Generates multiple alignment of variant calls | -- | - | Up-to-date | -https://snvphyl.readthedocs.io/en/latest/ | -Sequence Analysis | -vcf2snvalignment | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | verify_map | -1.8.2 | -1.8.2 | -snvphyl-tools | -Up-to-date | -- | - | - | - | Checks the mapping quality of all BAM(s) | -- | - | Up-to-date | -https://snvphyl.readthedocs.io/en/latest/ | -Sequence Analysis | -verify_map | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | suite_snvphyl | -- | - | - | To update | -- | - | - | - | SNVPhyl suite defining all dependencies for SNVPhyl | -- | - | To update | -- | Sequence Analysis | -suite_snvphyl_1_2_3 | -nml | -https://github.com/phac-nml/snvphyl-galaxy | -
- | cooler | -0.9.3 | -1.19.1 | -htslib | -To update | -- | - | - | - | cooler different tools to process Hi-C from mirnylab | -- | - | To update | -https://github.com/open2c/cooler | -Epigenetics | -cooler | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml | -
- | fromHicupToJuicebox | -0.0.2 | -0.22.0 | -pysam | -To update | -- | - | - | - | Convert the output of hicup (as sam or bam) to the input of juicebox. | -- | - | To update | -- | Epigenetics | -from_hicup_to_juicebox | -lldelisle | -- |
- | fromgtfTobed12 | -0.11.1+galaxy1 | -0.12 | -gffutils | -To update | -- | - | - | - | Convert GTF files to BED12 format | -- | - | To update | -https://pythonhosted.org/gffutils/contents.html | -Convert Formats | -fromgtftobed12 | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 | -
- | getTn5ExtendedCoverage | -0.0.2 | -0.22.0 | -pysam | -To update | -- | - | - | - | Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension | -- | - | To update | -- | Epigenetics | -gettn5extendedcoverage | -lldelisle | -- |
- | hyperstack_to_bleach_corrected_movie | -20230328 | -20231211 | -Fiji | -To update | -- | - | - | - | Generate blach corrected movie from hyperstack | -- | - | To update | -- | Imaging | -hyperstack_to_bleach_corrected_movie | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie | -
- | incucyte_stack_and_upload_omero | -20231221 | -20231211 | -Fiji | -To update | -- | - | - | - | Combine images to stack and upload to the omero server | -- | - | To update | -- | Imaging | -incucyte_stack_and_upload_omero | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero | -
- | measure_gastruloids | -20221216 | -20231211 | -fiji | -To update | -- | - | - | - | Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index | -- | - | To update | -- | Imaging | -measure_gastruloids | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids | -
- | omero_clean_rois_tables | -20230623 | -20231211 | -fiji | -To update | -- | - | - | - | Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down | -- | - | To update | -- | Imaging | -omero_clean_rois_tables | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables | -
- | omero_get_children_ids | -0.1.0 | -5.11.1 | -omero-py | -To update | -- | - | - | - | Get omero id of children of an omero object id | -- | - | To update | -- | Imaging | -omero_get_children_ids | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids | -
- | omero_hyperstack_to_fluo_measurements_on_gastruloid | -20230809 | -20231211 | -fiji | -To update | -- | - | - | - | Analyse Hyperstack on OMERO server to measure fluorescence levels | -- | - | To update | -- | Imaging | -omero_hyperstack_to_fluo_measurements_on_gastruloid | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid | -
- | omero_hyperstack_to_gastruloid_measurements | -20240214 | -20231211 | -fiji | -To update | -- | - | - | - | Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements | -- | - | To update | -- | Imaging | -omero_hyperstack_to_gastruloid_measurements | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements | -
- | revertR2orientationInBam | -0.0.2 | -1.19.2 | -samtools | -To update | -- | - | - | - | Revert the mapped orientation of R2 mates in a bam. | -- | - | To update | -- | SAM | -revertr2orientationinbam | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam | -
- | upload_roi_and_measures_to_omero | -0.0.5 | -5.11.1 | -omero-py | -To update | -- | - | - | - | Upload the ROI coordinates and the measurements to the omero server | -- | - | To update | -- | Imaging | -upload_roi_and_measures_to_omero | -lldelisle | -https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero | -
- | blast2go | -0.0.11 | -- | b2g4pipe | -To update | -- | - | - | - | Maps BLAST results to GO annotation terms | -- | - | To update | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go | -Ontology Manipulation, Sequence Analysis | -blast2go | -peterjc | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go | -
- | blast_rbh | -0.3.0 | -1.70 | -biopython | -To update | -- | - | - | - | BLAST Reciprocal Best Hits (RBH) from two FASTA files | -- | - | To update | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | -Fasta Manipulation, Sequence Analysis | -blast_rbh | -peterjc | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | -
- | blastxml_to_top_descr | -0.1.2 | -- | python | -To update | -- | - | - | - | Make table of top BLAST match descriptions | -- | - | To update | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr | -Convert Formats, Sequence Analysis, Text Manipulation | -blastxml_to_top_descr | -peterjc | -https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr | -
- | make_nr | -0.0.2 | -1.70 | -biopython | -To update | -- | - | - | - | Make a FASTA file non-redundant | -- | - | To update | -https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr | -Fasta Manipulation, Sequence Analysis | -make_nr | -peterjc | -https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr | -
- | ncbi_blast_plus | -2.14.1 | -- | python | -To update | -- | - | - | - | NCBI BLAST+ | -- | - | To update | -https://blast.ncbi.nlm.nih.gov/ | -Sequence Analysis | -ncbi_blast_plus | -devteam | -https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus | -