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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 22 20

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

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

    Python 128 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 14 10

  6. genome_uploader genome_uploader Public

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

    Python 20 4

Repositories

Showing 10 of 173 repositories
  • mgnify-ro-crates Public

    A library for creating browsable ro-crates for various pipeline results

    EBI-Metagenomics/mgnify-ro-crates’s past year of commit activity
    Python 0 0 0 0 Updated Nov 16, 2024
  • mett-dataportal Public
    EBI-Metagenomics/mett-dataportal’s past year of commit activity
    Python 0 0 0 0 Updated Nov 15, 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 1 Updated Nov 15, 2024
  • miassembler Public
    EBI-Metagenomics/miassembler’s past year of commit activity
    Nextflow 1 Apache-2.0 0 0 0 Updated Nov 15, 2024
  • HoloFoodR Public

    R interface for HoloFood resource

    EBI-Metagenomics/HoloFoodR’s past year of commit activity
    R 1 Artistic-2.0 1 3 1 Updated Nov 15, 2024
  • mgnify-pipelines-toolkit Public
    EBI-Metagenomics/mgnify-pipelines-toolkit’s past year of commit activity
    Python 0 Apache-2.0 1 0 0 Updated Nov 15, 2024
  • hmmer3 Public

    HMMER (version 3) related projects

    EBI-Metagenomics/hmmer3’s past year of commit activity
    C 1 0 0 0 Updated Nov 15, 2024
  • genomes-generation Public
    EBI-Metagenomics/genomes-generation’s past year of commit activity
    Nextflow 2 Apache-2.0 0 0 1 Updated Nov 15, 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 Nov 14, 2024
  • taxdb_generation_nf Public
    EBI-Metagenomics/taxdb_generation_nf’s past year of commit activity
    Perl 0 Apache-2.0 0 0 0 Updated Nov 14, 2024
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