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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 19

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

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

    Python 124 16

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

    MGnify genome analysis pipeline

    Python 99 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 167 repositories
  • emg-viral-pipeline Public

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

    EBI-Metagenomics/emg-viral-pipeline’s past year of commit activity
    Python 124 Apache-2.0 16 20 (1 issue needs help) 4 Updated Oct 10, 2024
  • mett-dataportal Public
    EBI-Metagenomics/mett-dataportal’s past year of commit activity
    Python 0 0 0 0 Updated Oct 10, 2024
  • mettannotator Public
    EBI-Metagenomics/mettannotator’s past year of commit activity
    Python 53 Apache-2.0 5 2 (1 issue needs help) 1 Updated Oct 10, 2024
  • mobilome-annotation-pipeline Public
    EBI-Metagenomics/mobilome-annotation-pipeline’s past year of commit activity
    Python 24 Apache-2.0 0 3 0 Updated Oct 10, 2024
  • containers Public

    Repository to contain containers used by EBI Microbiome Informatics

    EBI-Metagenomics/containers’s past year of commit activity
    Python 0 0 0 4 Updated Oct 9, 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 11 Updated Oct 9, 2024
  • MGnifyR Public

    R package for searching, downloading and analysis of EBI MGnify metagenomics data

    EBI-Metagenomics/MGnifyR’s past year of commit activity
    R 19 Artistic-2.0 11 4 0 Updated Oct 9, 2024
  • nf-modules Public

    Microbiome Informatics NF modules and sufworkflows

    EBI-Metagenomics/nf-modules’s past year of commit activity
    JavaScript 4 0 0 4 Updated Oct 8, 2024
  • mgnifams-site Public
    EBI-Metagenomics/mgnifams-site’s past year of commit activity
    JavaScript 1 MIT 1 0 0 Updated Oct 8, 2024
  • mgnify-pipelines-toolkit Public
    EBI-Metagenomics/mgnify-pipelines-toolkit’s past year of commit activity
    Python 0 Apache-2.0 1 0 1 Updated Oct 8, 2024
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