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@EBI-Metagenomics MGnify

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    206 repositories

    • mett-dataportal

      Public
      Python
      •0•0•0•0•Updated Feb 2, 2026Feb 2, 2026

    • emgapi-v2

      Public
      MGnify API (v2) and production automation system
      apiautomationdjangoslurmmetagenomicsprefect
      HTML
      •1•2•0•10•Updated Feb 2, 2026Feb 2, 2026

    • amplicon-analysis-pipeline

      Public
      Nextflow
      •
      Apache License 2.0
      •2•7•0•1•Updated Feb 2, 2026Feb 2, 2026

    • nf-modules

      Public
      Microbiome Informatics NF modules and subworkflows
      JavaScript
      •
      Apache License 2.0
      •1•5•0•1•Updated Feb 2, 2026Feb 2, 2026

    • mgnipy

      Public
      a python sdk for the MGnify API
      openapimgnifymetagenomics-data
      Python
      •
      GNU General Public License v3.0
      •0•0•11•0•Updated Feb 1, 2026Feb 1, 2026

    • mgnify-pipelines-toolkit

      Public
      This Python package contains a collection of scripts and tools for including in MGnify pipelines
      Python
      •
      Apache License 2.0
      •2•1•0•1•Updated Jan 28, 2026Jan 28, 2026

    • nextflow-in-an-hour

      Public
      Nextflow
      •
      MIT License
      •0•3•0•0•Updated Jan 28, 2026Jan 28, 2026

    • prefect-slurm

      Public
      Prefect worker to run flows on a Slurm HPC cluster
      Python
      •
      Apache License 2.0
      •1•15•0•1•Updated Jan 27, 2026Jan 27, 2026

    • containers

      Public
      Repository to contain containers used by EBI Microbiome Informatics
      Python
      •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

    • mgnify-jbrowse

      Public
      TypeScript
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

    • miassembler

      Public
      Nextflow
      •
      Apache License 2.0
      •0•4•0•0•Updated Jan 26, 2026Jan 26, 2026

    • assembly-analysis-pipeline

      Public
      MGnify Assembly Analysis Pipeline
      sciencepipelinegenomicsnextflowmetagenomics
      JavaScript
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 23, 2026Jan 23, 2026

    • datascout

      Public
      This repo queries and gather data from different resources which can then be used to run bulk automatised annotation of microbial genomes.The different types of…
      Standard ML
      •
      MIT License
      •0•0•4•0•Updated Jan 23, 2026Jan 23, 2026

    • mett-dataportal-client

      Public
      ME TT Data Portal Client
      Python
      •0•0•0•0•Updated Jan 22, 2026Jan 22, 2026

    • ebi-metagenomics-client

      Public
      This repos contains the MGnify web client
      javascriptclientwebsitewebpackbackbone
      TypeScript
      •1•4•0•18•Updated Jan 22, 2026Jan 22, 2026

    • metaViraVerse

      Public
      Viral catalogue generation pipeline
      Python
      •
      MIT License
      •0•0•0•2•Updated Jan 20, 2026Jan 20, 2026

    • kegg-pathways-completeness-tool

      Public
      This tool estimates the completeness of KEGG pathway modules from the presence or absence of KEGG orthologues (KOs)
      Python
      •
      Apache License 2.0
      •6•30•0•0•Updated Jan 19, 2026Jan 19, 2026

    • mgnify-branchwater

      Public
      Python
      •
      Other
      •0•0•0•2•Updated Jan 19, 2026Jan 19, 2026

    • mobilome-annotation-pipeline

      Public
      Python
      •
      Apache License 2.0
      •5•82•2•0•Updated Jan 16, 2026Jan 16, 2026

    • raw-reads-analysis-pipeline

      Public
      Raw Reads Analysis Pipeline
      Nextflow
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 15, 2026Jan 15, 2026

    • MAG-to-assembly-pipeline

      Public
      Nextflow pipeline that wraps the assembly-MAG linking script
      0•0•0•0•Updated Jan 15, 2026Jan 15, 2026

    • genome_uploader

      Public
      Python script to upload bins and MAGs to ENA (European Nucleotide Archive)
      Python
      •
      Apache License 2.0
      •5•25•0•1•Updated Jan 14, 2026Jan 14, 2026

    • genomes-catalogue-pipeline

      Public
      MGnify genome analysis pipeline
      Python
      •
      Other
      •22•108•9•3•Updated Jan 9, 2026Jan 9, 2026

    • MGnifyR

      Public
      R package for searching, downloading and analysis of EBI MGnify metagenomics data
      R
      •
      Artistic License 2.0
      •10•23•7•0•Updated Jan 9, 2026Jan 9, 2026

    • genome-assembly-linkage-phase2

      Public
      Branchwater result processing for Phase 2 of MGnify genome–assembly linkage.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 1, 2026Jan 1, 2026

    • genomes-generation

      Public
      Nextflow
      •
      Apache License 2.0
      •0•3•4•1•Updated Dec 22, 2025Dec 22, 2025

    • hmmer

      Public
      HMMER: biological sequence analysis using profile HMMs
      C
      •
      Other
      •89•0•0•0•Updated Dec 22, 2025Dec 22, 2025

    • metagenomics_amplicon_soil_practical_2025

      Public
      SCSS
      •
      Apache License 2.0
      •4•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • emg-viral-pipeline

      Public
      VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
      workflowpipelinenextflowvirusescwl
      Python
      •
      Apache License 2.0
      •21•146•13•0•Updated Dec 17, 2025Dec 17, 2025

    • mgnify-sourmash-component

      Public
      A web component that let you select FastA or FastQ sequence files and creates sketches (KmerMinHash signatures) using Sourmash.
      metagenomicssourmashmgnify
      TypeScript
      •3•2•1•1•Updated Dec 14, 2025Dec 14, 2025