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@EBI-Metagenomics

MGnify

MGnify (formerly known as EBImetagenomics) is a free resource for the assembly, analysis, archiving and browsing all types of microbiome derived sequence data

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  1. pipeline-v5 pipeline-v5 Public

    This repository contains all CWL descriptions of the MGnify pipeline version 5.0.

    HTML 21 20

  2. emg-viral-pipeline emg-viral-pipeline Public

    VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

    Python 125 16

  3. genomes-catalogue-pipeline genomes-catalogue-pipeline Public

    MGnify genome analysis pipeline

    Python 100 21

  4. mgnify-web mgnify-web Public

    Parent repo for MGnify's (EMBL-EBI's metagenomics platform) API and web client. Designed for local development.

    Python 5

  5. notebooks notebooks Public

    MGnify documentation and Jupyter Lab notebooks to support downstream analysis of MGnify data (EMBL-EBI's metagenomics platform)

    Jupyter Notebook 13 10

  6. genome_uploader genome_uploader Public

    Python script to upload bins and MAGs to ENA (European Nucleotide Archive)

    Python 20 3

Repositories

Showing 10 of 170 repositories
  • amplicon-pipeline Public
    EBI-Metagenomics/amplicon-pipeline’s past year of commit activity
    Nextflow 4 Apache-2.0 1 0 0 Updated Oct 22, 2024
  • mett-dataportal Public
    EBI-Metagenomics/mett-dataportal’s past year of commit activity
    TypeScript 0 0 0 0 Updated Oct 22, 2024
  • HoloFoodR Public

    R interface for HoloFood resource

    EBI-Metagenomics/HoloFoodR’s past year of commit activity
    R 1 Artistic-2.0 1 3 0 Updated Oct 22, 2024
  • nf-modules Public

    Microbiome Informatics NF modules and sufworkflows

    EBI-Metagenomics/nf-modules’s past year of commit activity
    JavaScript 4 1 0 4 Updated Oct 22, 2024
  • emgapi Public

    MGnify RESTful API

    EBI-Metagenomics/emgapi’s past year of commit activity
    Python 10 Apache-2.0 0 5 8 Updated Oct 21, 2024
  • MAG-to-assembly-pipeline Public

    Nextflow pipeline that wraps the assembly-MAG linking script

    EBI-Metagenomics/MAG-to-assembly-pipeline’s past year of commit activity
    0 0 0 0 Updated Oct 21, 2024
  • genomes-catalogue-pipeline Public

    MGnify genome analysis pipeline

    EBI-Metagenomics/genomes-catalogue-pipeline’s past year of commit activity
    Python 100 21 7 2 Updated Oct 21, 2024
  • shallowmapping Public

    Shallow-shotgun mapping pipeline

    EBI-Metagenomics/shallowmapping’s past year of commit activity
    Python 0 MIT 0 1 1 Updated Oct 21, 2024
  • ebi-metagenomics-client Public

    This repos contains the MGnify web client

    EBI-Metagenomics/ebi-metagenomics-client’s past year of commit activity
    TypeScript 4 1 0 10 Updated Oct 20, 2024
  • genomes-generation Public
    EBI-Metagenomics/genomes-generation’s past year of commit activity
    Nextflow 1 Apache-2.0 0 0 1 Updated Oct 18, 2024
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