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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 18

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

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

    Python 109 13

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

    MGnify genome analysis pipeline

    Python 92 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 10 9

  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 160 repositories
  • mettannotator Public
    EBI-Metagenomics/mettannotator’s past year of commit activity
    Python 3 Apache-2.0 2 0 0 Updated Jul 2, 2024
  • fetch_tool Public

    Tool which allows you to fetch RAW read files from the European Nucleotide Archive (ENA)

    EBI-Metagenomics/fetch_tool’s past year of commit activity
    Python 2 Apache-2.0 2 4 1 Updated Jul 1, 2024
  • miassembler Public
    EBI-Metagenomics/miassembler’s past year of commit activity
    Nextflow 0 Apache-2.0 0 0 1 Updated Jul 1, 2024
  • mgnifams Public
    EBI-Metagenomics/mgnifams’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Jul 1, 2024
  • kegg-pathways-completeness-tool Public
    EBI-Metagenomics/kegg-pathways-completeness-tool’s past year of commit activity
    Python 8 Apache-2.0 2 1 2 Updated Jul 1, 2024
  • nf-modules Public

    Microbiome Informatics NF modules and sufworkflows

    EBI-Metagenomics/nf-modules’s past year of commit activity
    Nextflow 3 0 0 3 Updated Jun 28, 2024
  • HoloFoodR Public

    R interface for HoloFood resource

    EBI-Metagenomics/HoloFoodR’s past year of commit activity
    R 1 Artistic-2.0 0 3 0 Updated Jun 27, 2024
  • genome_uploader Public

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

    EBI-Metagenomics/genome_uploader’s past year of commit activity
    Python 20 Apache-2.0 3 0 0 Updated Jun 27, 2024
  • mgnifams-site Public
    EBI-Metagenomics/mgnifams-site’s past year of commit activity
    JavaScript 1 MIT 1 0 0 Updated Jun 27, 2024
  • causal_multi-omics_recommender Public
    EBI-Metagenomics/causal_multi-omics_recommender’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Jun 26, 2024
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