MGnify

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177 repositories

miassembler
Public
Nextflow
•
Apache License 2.0
•0•1•0•1•Updated Feb 5, 2025Feb 5, 2025
mett-dataportal
Public
TypeScript
•0•0•0•0•Updated Feb 5, 2025Feb 5, 2025
emgapi-v2
Public
MGnify API (v2) and production automation system
api automation django slurm metagenomics prefect
Python
•1•0•0•1•Updated Feb 5, 2025Feb 5, 2025
genome-properties-bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
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MIT License
•3.3k•0•0•0•Updated Feb 5, 2025Feb 5, 2025
emg-viral-pipeline
Public
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
workflow pipeline nextflow viruses cwl
Python
•
Apache License 2.0
•16•129•19•2•Updated Feb 5, 2025Feb 5, 2025
amplicon-pipeline
Public
Nextflow
•
Apache License 2.0
•1•6•0•0•Updated Feb 5, 2025Feb 5, 2025
mobilome-annotation-pipeline
Public
Python
•
Apache License 2.0
•1•31•2•0•Updated Feb 4, 2025Feb 4, 2025
ebi-metagenomics-client
Public
This repos contains the MGnify web client
javascript client website webpack backbone
TypeScript
•1•4•0•8•Updated Feb 4, 2025Feb 4, 2025
assembly-analysis-pipeline
Public
Nextflow
•
Apache License 2.0
•0•0•0•0•Updated Feb 3, 2025Feb 3, 2025
fetch_tool
Public
Tool which allows you to fetch RAW read files from the European Nucleotide Archive (ENA)
Python
•
Apache License 2.0
•2•2•4•0•Updated Feb 3, 2025Feb 3, 2025
containers
Public
Repository to contain containers used by EBI Microbiome Informatics
Python
•0•0•0•0•Updated Jan 31, 2025Jan 31, 2025
EukCC
Public
Tool to estimate genome quality of microbial eukaryotes
Python
•
GNU General Public License v3.0
•9•36•20•0•Updated Jan 31, 2025Jan 31, 2025
.github
Public
0•0•0•0•Updated Jan 31, 2025Jan 31, 2025
genomes-generation
Public
Nextflow
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Apache License 2.0
•0•2•0•2•Updated Jan 31, 2025Jan 31, 2025
mgnifams
Public
Python
•
Apache License 2.0
•0•1•0•0•Updated Jan 31, 2025Jan 31, 2025
genome-properties-api
Public
Python
•0•0•0•1•Updated Jan 31, 2025Jan 31, 2025
notebooks
Public
MGnify documentation and Jupyter Lab notebooks to support downstream analysis of MGnify data (EMBL-EBI's metagenomics platform)
python documentation metagenomics comparative-genomics notebooks rlang quarto shinyproxy jupyterlab-extension biohackeu22
Jupyter Notebook
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Apache License 2.0
•10•14•3•6•Updated Jan 31, 2025Jan 31, 2025
assembly_uploader
Public
Upload of metagenome and metatranscriptome assemblies to ENA
Python
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Apache License 2.0
•0•0•0•0•Updated Jan 31, 2025Jan 31, 2025
emgapi
Public
MGnify RESTful API
api django resource django-rest-framework jsonapi
Python
•
Apache License 2.0
•0•10•4•2•Updated Jan 31, 2025Jan 31, 2025
genome-properties-viewer
Public
JavaScript
•0•0•0•0•Updated Jan 31, 2025Jan 31, 2025
CWL_binning
Public archive
Common Workflow Language
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Apache License 2.0
•1•0•0•0•Updated Jan 31, 2025Jan 31, 2025
emg-toolkit
Public
MGnify API toolkit
python bioinformatics metagenomics-toolkit
Python
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Apache License 2.0
•4•21•7•0•Updated Jan 31, 2025Jan 31, 2025
ena-api-handler
Public
Python
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Apache License 2.0
•2•1•0•1•Updated Jan 31, 2025Jan 31, 2025
mgnify-pipelines-toolkit
Public
Python
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Apache License 2.0
•1•0•0•0•Updated Jan 30, 2025Jan 30, 2025
nf-modules
Public
Microbiome Informatics NF modules and sufworkflows
JavaScript
•1•4•0•1•Updated Jan 29, 2025Jan 29, 2025
genome_uploader-bioconda-recipes
Public
Conda recipes for MGnify's genome uploader
Shell
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MIT License
•3.3k•0•0•0•Updated Jan 29, 2025Jan 29, 2025
kegg-pathways-completeness-tool
Public
Python
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Apache License 2.0
•4•16•0•0•Updated Jan 28, 2025Jan 28, 2025
genomes-catalogue-pipeline
Public
MGnify genome analysis pipeline
Python
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Other
•21•104•7•1•Updated Jan 28, 2025Jan 28, 2025
genome_uploader
Public
Python script to upload bins and MAGs to ENA (European Nucleotide Archive)
Python
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Apache License 2.0
•4•23•0•1•Updated Jan 27, 2025Jan 27, 2025
motus_pipeline
Public
Raw reads mOTUs and taxonomic classification pipeline
HTML
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Apache License 2.0
•0•3•0•1•Updated Jan 27, 2025Jan 27, 2025