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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 114 15

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

    MGnify genome analysis pipeline

    Python 93 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 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 162 repositories
  • genomes-catalogue-pipeline Public

    MGnify genome analysis pipeline

    EBI-Metagenomics/genomes-catalogue-pipeline’s past year of commit activity
    Python 93 21 7 4 Updated Jul 30, 2024
  • mgnify-pipelines-toolkit Public
    EBI-Metagenomics/mgnify-pipelines-toolkit’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Jul 30, 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 1 Updated Jul 30, 2024
  • genomes-generation Public
    EBI-Metagenomics/genomes-generation’s past year of commit activity
    Nextflow 0 Apache-2.0 0 0 1 Updated Jul 30, 2024
  • miassembler Public
    EBI-Metagenomics/miassembler’s past year of commit activity
    Nextflow 0 Apache-2.0 0 0 0 Updated Jul 29, 2024
  • assembly_uploader Public

    Upload of metagenome and metatranscriptome assemblies to ENA

    EBI-Metagenomics/assembly_uploader’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Jul 29, 2024
  • amplicon-pipeline Public
    EBI-Metagenomics/amplicon-pipeline’s past year of commit activity
    Nextflow 4 Apache-2.0 0 0 0 Updated Jul 26, 2024
  • notebooks Public

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

    EBI-Metagenomics/notebooks’s past year of commit activity
    Jupyter Notebook 10 Apache-2.0 10 3 5 Updated Jul 26, 2024
  • mgnifams Public
    EBI-Metagenomics/mgnifams’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Jul 24, 2024
  • mettannotator Public
    EBI-Metagenomics/mettannotator’s past year of commit activity
    Python 33 Apache-2.0 4 1 0 Updated Jul 23, 2024
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