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@EBI-Metagenomics MGnify

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    175 repositories

    • mgnify-pipelines-toolkit

      Public
      Python
      •
      Apache License 2.0
      •1•0•0•1•Updated Jan 25, 2025Jan 25, 2025

    • assembly-analysis-pipeline

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

    • emgapi-v2

      Public
      MGnify API (v2) and production automation system
      apiautomationdjangoslurmmetagenomicsprefect
      Python
      •0•0•1•2•Updated Jan 24, 2025Jan 24, 2025

    • miassembler

      Public
      Nextflow
      •
      Apache License 2.0
      •0•1•0•1•Updated Jan 24, 2025Jan 24, 2025

    • emg-viral-pipeline

      Public
      VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
      workflowpipelinenextflowvirusescwl
      Python
      •
      Apache License 2.0
      •16•128•19•3•Updated Jan 24, 2025Jan 24, 2025

    • containers

      Public
      Repository to contain containers used by EBI Microbiome Informatics
      Python
      •0•0•0•1•Updated Jan 24, 2025Jan 24, 2025

    • genomes-catalogue-pipeline

      Public
      MGnify genome analysis pipeline
      Python
      •
      Other
      •21•104•7•1•Updated Jan 24, 2025Jan 24, 2025

    • genomes-generation

      Public
      Nextflow
      •
      Apache License 2.0
      •0•2•0•1•Updated Jan 24, 2025Jan 24, 2025

    • kegg-pathways-completeness-tool

      Public
      Python
      •
      Apache License 2.0
      •4•16•1•1•Updated Jan 24, 2025Jan 24, 2025

    • mett-dataportal

      Public
      TypeScript
      •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • EukCC

      Public
      Tool to estimate genome quality of microbial eukaryotes
      Python
      •
      GNU General Public License v3.0
      •9•35•20•1•Updated Jan 23, 2025Jan 23, 2025

    • nf-modules

      Public
      Microbiome Informatics NF modules and sufworkflows
      JavaScript
      •1•4•0•2•Updated Jan 23, 2025Jan 23, 2025

    • deciphon

      Public
      Deciphon related projects
      C
      •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • hmmer3

      Public
      HMMER (version 3) related projects
      C
      •0•1•0•0•Updated Jan 23, 2025Jan 23, 2025

    • combined-gene-caller

      Public
      MGnify combined gene caller tool
      bioinformaticsmetagenomics
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

    • amplicon-pipeline

      Public
      Nextflow
      •
      Apache License 2.0
      •1•6•0•2•Updated Jan 14, 2025Jan 14, 2025

    • holofood-database

      Public
      HoloFood is a project investigating sustainable food production through hologenomics. This Django app is the data portal where samples and other datasets from the project are made publicly available.
      pythonmetagenomicsmetabolomicsomics
      Python
      •
      Apache License 2.0
      •0•1•1•0•Updated Jan 13, 2025Jan 13, 2025

    • mgnifams

      Public
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Jan 13, 2025Jan 13, 2025

    • ebi-metagenomics-client

      Public
      This repos contains the MGnify web client
      javascriptclientwebsitewebpackbackbone
      TypeScript
      •1•4•0•10•Updated Jan 8, 2025Jan 8, 2025

    • shallowmapping

      Public
      Shallow-shotgun mapping pipeline
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

    • genome_uploader

      Public
      Python script to upload bins and MAGs to ENA (European Nucleotide Archive)
      Python
      •
      Apache License 2.0
      •4•23•0•3•Updated Dec 27, 2024Dec 27, 2024

    • mettannotator

      Public
      Python
      •
      Apache License 2.0
      •5•60•0•0•Updated Dec 23, 2024Dec 23, 2024

    • mgnifams-site

      Public
      JavaScript
      •
      MIT License
      •1•2•0•0•Updated Dec 23, 2024Dec 23, 2024

    • taxdb_generation_nf

      Public
      Perl
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • mobilome-annotation-pipeline

      Public
      Python
      •
      Apache License 2.0
      •1•30•2•0•Updated Dec 16, 2024Dec 16, 2024

    • assembly_uploader

      Public
      Upload of metagenome and metatranscriptome assemblies to ENA
      Python
      •
      Apache License 2.0
      •0•0•0•1•Updated Dec 12, 2024Dec 12, 2024

    • MAG-to-assembly-pipeline

      Public
      Nextflow pipeline that wraps the assembly-MAG linking script
      0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

    • ena-api-handler

      Public
      Python
      •
      Apache License 2.0
      •2•1•0•2•Updated Dec 3, 2024Dec 3, 2024

    • MGnifyR

      Public
      R package for searching, downloading and analysis of EBI MGnify metagenomics data
      R
      •
      Artistic License 2.0
      •10•19•4•0•Updated Dec 2, 2024Dec 2, 2024

    • HoloFoodR

      Public
      R interface for HoloFood resource
      R
      •
      Artistic License 2.0
      •1•1•3•0•Updated Dec 2, 2024Dec 2, 2024