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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 102 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 22 4

Repositories

Showing 10 of 175 repositories
  • kegg-pathways-completeness-tool Public
    EBI-Metagenomics/kegg-pathways-completeness-tool’s past year of commit activity
    Python 16 Apache-2.0 3 1 2 Updated Jan 13, 2025
  • mett-dataportal Public
    EBI-Metagenomics/mett-dataportal’s past year of commit activity
    TypeScript 0 0 0 0 Updated Jan 13, 2025
  • holofood-database Public

    HoloFood is a project investigating sustainable food production through hologenomics. This Django app is the data portal where samples and other datasets from the project are made publicly available.

    EBI-Metagenomics/holofood-database’s past year of commit activity
    Python 1 Apache-2.0 0 1 0 Updated Jan 13, 2025
  • mgnifams Public
    EBI-Metagenomics/mgnifams’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Jan 13, 2025
  • emgapi-v2 Public

    MGnify API (v2) and production automation system

    EBI-Metagenomics/emgapi-v2’s past year of commit activity
    Python 0 0 1 3 Updated Jan 11, 2025
  • assembly-analysis-pipeline Public
    EBI-Metagenomics/assembly-analysis-pipeline’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Jan 10, 2025
  • mgnify-pipelines-toolkit Public
    EBI-Metagenomics/mgnify-pipelines-toolkit’s past year of commit activity
    Python 0 Apache-2.0 1 0 0 Updated Jan 10, 2025
  • EukCC Public

    Tool to estimate genome quality of microbial eukaryotes

    EBI-Metagenomics/EukCC’s past year of commit activity
    Python 35 GPL-3.0 9 25 1 Updated Jan 9, 2025
  • 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 Jan 8, 2025
  • shallowmapping Public

    Shallow-shotgun mapping pipeline

    EBI-Metagenomics/shallowmapping’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Jan 6, 2025
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