MGnify

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178 repositories

emgapi-v2
Public
MGnify API (v2) and production automation system
api automation django slurm metagenomics prefect
Python
•1•1•0•4•Updated Feb 14, 2025Feb 14, 2025
assembly-analysis-pipeline
Public
JavaScript
•
Apache License 2.0
•0•0•0•0•Updated Feb 14, 2025Feb 14, 2025
nf-modules
Public
Microbiome Informatics NF modules and sufworkflows
JavaScript
•1•4•0•2•Updated Feb 14, 2025Feb 14, 2025
taxdb_generation_nf
Public
Perl
•
Apache License 2.0
•0•0•0•1•Updated Feb 14, 2025Feb 14, 2025
amplicon-pipeline
Public
Nextflow
•
Apache License 2.0
•1•6•0•0•Updated Feb 14, 2025Feb 14, 2025
mgnifams
Public
Python
•
Apache License 2.0
•0•1•0•0•Updated Feb 14, 2025Feb 14, 2025
mett-dataportal
Public
TypeScript
•0•0•0•0•Updated Feb 13, 2025Feb 13, 2025
mgnify-pipelines-toolkit
Public
Python
•
Apache License 2.0
•1•0•0•0•Updated Feb 13, 2025Feb 13, 2025
mobilome-annotation-pipeline
Public
Python
•
Apache License 2.0
•1•32•2•0•Updated Feb 13, 2025Feb 13, 2025
deciphon
Public
Deciphon related projects
C
•0•0•0•0•Updated Feb 11, 2025Feb 11, 2025
hmmer3
Public
HMMER (version 3) related projects
C
•0•1•0•0•Updated Feb 10, 2025Feb 10, 2025
pydantic-ro-crates
Public
A Python library that uses Pydantic and Schema.org to help crate RO-Crates (metadata packaged research objects)
python open-science schema-org research-object fair-data pydantic biohackathon-europe ro-crate biohackeu24
Python
•
Apache License 2.0
•0•2•0•0•Updated Feb 9, 2025Feb 9, 2025
genomes-catalogue-pipeline
Public
MGnify genome analysis pipeline
Python
•
Other
•21•104•7•1•Updated Feb 9, 2025Feb 9, 2025
miassembler
Public
Nextflow
•
Apache License 2.0
•0•1•0•0•Updated Feb 7, 2025Feb 7, 2025
genomes-generation
Public
Nextflow
•
Apache License 2.0
•0•2•0•2•Updated Feb 6, 2025Feb 6, 2025
containers
Public
Repository to contain containers used by EBI Microbiome Informatics
Python
•0•0•0•1•Updated Feb 6, 2025Feb 6, 2025
genome-properties-bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
•
MIT License
•3.4k•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•130•19•2•Updated Feb 5, 2025Feb 5, 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
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
EukCC
Public
Tool to estimate genome quality of microbial eukaryotes
Python
•
GNU General Public License v3.0
•9•36•21•0•Updated Jan 31, 2025Jan 31, 2025
.github
Public
0•0•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
•
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
•
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
•
Apache License 2.0
•4•21•7•0•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