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software_versions.tsv
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software_versions.tsv
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resource type description version step in metaGOflow official_url Docker pull command
fetch_tool software Allows to download data from ENA 1 - https://github.com/EBI-Metagenomics/fetch_tool hariszaf/fetch-tool:latest
debian_slim OS Debian is a Linux distribution that's composed entirely of free and open-source software 11.5 taxonomy inventory https://www.debian.org/releases/ debian:stable-slim
fastp software 0.20.0 quality control https://github.com/OpenGene/fastp microbiomeinformatics/pipeline-v5.fastp:0.20.0
easel software computational analysis of biological sequences using probabilistic models. Easel is used by HMMER, the profile hidden Markov model software that underlies several protein and DNA sequence family databases such as Pfam, and by Infernal, 0.45h taxonomy inventory https://github.com/EddyRivasLab/easel microbiomeinformatics/pipeline-v5.easel:v0.45h
python3 programming language a high-level, general-purpose programming language 3.3 - https://www.python.org microbiomeinformatics/pipeline-v5.python3:v3.1
python2 programming language a high-level, general-purpose programming language 2.7.10 - https://www.python.org microbiomeinformatics/pipeline-v5.python2:v1
bash-scripts script set of stand-alone scripts for several tasks 1.3 taxonomy inventory https://hub.docker.com/r/microbiomeinformatics/pipeline-v5.bash-scripts microbiomeinformatics/pipeline-v5.bash-scripts:v1.3
cmsearch software earch CM(s) against a nucleotide sequence database, using profile HMM(s) to prefilter the database. 1.1.2 taxonomy inventory https://github.com/EddyRivasLab/infernal microbiomeinformatics/pipeline-v5.cmsearch:v1.1.2
cmsearch-deoverlap software convert cmsearch output 0.02 taxonomy inventory https://github.com/nawrockie/cmsearch_tblout_deoverlap microbiomeinformatics/pipeline-v5.cmsearch-deoverlap:v0.02
alpine OS Alpine Linux is a security-oriented, lightweight Linux distribution based on musl libc and busybox. 3.7 taxonomy inventory, CGC https://www.alpinelinux.org alpine:3.7
mapseq software a set of fast and accurate sequence read classification tools designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. 1.2.3 taxonomy inventory https://github.com/jfmrod/MAPseq microbiomeinformatics/pipeline-v5.mapseq:v1.2.3
mapseq2biom software convert mapseq output 1 taxonomy inventory https://github.com/EBI-Metagenomics/pipeline-v5/blob/develop/tools/RNA_prediction/mapseq2biom/mapseq2biom.pl microbiomeinformatics/pipeline-v5.mapseq2biom:v1.0
KronaTools software Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. 2.7.1 taxonomy inventory https://github.com/marbl/Krona microbiomeinformatics/pipeline-v5.krona:v2.7.1
biom convert software Biom convert wrapper 2.1.6 taxonomy inventory https://pypi.org/project/biom-format/ microbiomeinformatics/pipeline-v5.biom-convert:v2.1.6
FragGeneScan software FragGeneScan is an application for finding (fragmented) genes in short reads. 1.31 CGC https://github.com/EBI-Metagenomics/fraggenescan hariszaf/pipeline-v5.fraggenescan:v1.31.1
Combined Gene Caller software script from the MGnify group for post-processing of FGS and Prodigal 1.0.1 CGC https://github.com/EBI-Metagenomics/pipeline-v5/tree/pipeline_5.1/tools/Combined_gene_caller microbiomeinformatics/pipeline-v5.protein-post-processing:v1.0.1
eggNOG-mapper software 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. 2.18 functional annotation https://github.com/eggnogdb/eggnog-mapper/ hariszaf/pipeline-v5.eggnog:v2.1.8
interproscan database InterPro is a database which integrates together predictive information about proteins’ function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains. 5.57-90.0 functional annotation https://github.com/ebi-pf-team/interproscan hariszaf/pipeline-v5.interproscan:v5.57-90.0
hmmer software HMMER searches biological sequence databases for homologous sequences, using either single sequences or multiple sequence alignments as queries. HMMER implements a technology called "profile hidden Markov models" (profile HMMs). 3.2.1 functional annotation https://github.com/EddyRivasLab/hmmer microbiomeinformatics/pipeline-v5.hmmer:v3.2.1
megahit software MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly. 1.2.9 assembly https://github.com/voutcn/megahit quay.io/biocontainers/megahit:1.2.9--h2e03b76_1
mOTUs software The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data. 2.5.1 taxonomy inventory https://github.com/motu-tool/mOTUs microbiomeinformatics/pipeline-v5.motus:v2.5.1
GO-slim script Format IPS output 1.0.0 functional annotation https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/GO-slim/go_summary_pipeline-1.0.py microbiomeinformatics/pipeline-v5.go-summary:v1.0