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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 98 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
  • deciphon_web Public

    React webapp to submit and retrieve jobs from Deciphon – a protein prediction tool for nanopore reads

    EBI-Metagenomics/deciphon_web’s past year of commit activity
    JavaScript 0 Apache-2.0 1 0 0 Updated Oct 4, 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 4, 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 13 Apache-2.0 10 3 6 Updated Oct 4, 2024
  • mett-dataportal Public
    EBI-Metagenomics/mett-dataportal’s past year of commit activity
    Python 0 0 0 0 Updated Oct 4, 2024
  • 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) 3 Updated Oct 4, 2024
  • mgnifams-site Public
    EBI-Metagenomics/mgnifams-site’s past year of commit activity
    JavaScript 1 MIT 1 0 0 Updated Oct 4, 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 0 Updated Oct 3, 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 Oct 3, 2024
  • deciphon Public

    Deciphon related projects

    EBI-Metagenomics/deciphon’s past year of commit activity
    C 0 0 0 0 Updated Oct 3, 2024
  • nf-modules Public

    Microbiome Informatics NF modules and sufworkflows

    EBI-Metagenomics/nf-modules’s past year of commit activity
    JavaScript 4 0 0 3 Updated Oct 2, 2024
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