MGnify

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177 repositories

assembly-analysis-pipeline
Public
Nextflow
•
MIT License
•0•0•0•0•Updated Feb 1, 2025Feb 1, 2025
emgapi-v2
Public
MGnify API (v2) and production automation system
api automation django slurm metagenomics prefect
Python
•1•0•1•2•Updated Jan 31, 2025Jan 31, 2025
amplicon-pipeline
Public
Nextflow
•
Apache License 2.0
•1•6•0•0•Updated Jan 31, 2025Jan 31, 2025
containers
Public
Repository to contain containers used by EBI Microbiome Informatics
Python
•0•0•0•0•Updated Jan 31, 2025Jan 31, 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 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
mett-dataportal
Public
TypeScript
•0•0•0•0•Updated Jan 31, 2025Jan 31, 2025
.github
Public
0•0•0•0•Updated Jan 31, 2025Jan 31, 2025
genomes-generation
Public
Nextflow
•
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
ebi-metagenomics-client
Public
This repos contains the MGnify web client
javascript client website webpack backbone
TypeScript
•1•4•0•6•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
•
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
fetch_tool
Public
Tool which allows you to fetch RAW read files from the European Nucleotide Archive (ENA)
Python
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Apache License 2.0
•2•2•4•1•Updated Jan 31, 2025Jan 31, 2025
ena-api-handler
Public
Python
•
Apache License 2.0
•2•1•0•1•Updated Jan 31, 2025Jan 31, 2025
mgnify-pipelines-toolkit
Public
Python
•
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
emg-viral-pipeline
Public
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
workflow pipeline nextflow viruses cwl
Python
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Apache License 2.0
•16•128•19•3•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
miassembler
Public
Nextflow
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Apache License 2.0
•0•1•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
deciphon
Public
Deciphon related projects
C
•0•0•0•0•Updated Jan 23, 2025Jan 23, 2025