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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 103 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
  • 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 128 Apache-2.0 16 20 (1 issue needs help) 3 Updated Jan 16, 2025
  • mett-dataportal Public
    EBI-Metagenomics/mett-dataportal’s past year of commit activity
    TypeScript 0 0 0 0 Updated Jan 16, 2025
  • combined-gene-caller Public

    MGnify combined gene caller tool

    EBI-Metagenomics/combined-gene-caller’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Jan 15, 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 0 Updated Jan 15, 2025
  • nf-modules Public

    Microbiome Informatics NF modules and sufworkflows

    EBI-Metagenomics/nf-modules’s past year of commit activity
    JavaScript 4 1 0 3 Updated Jan 15, 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 20 0 Updated Jan 15, 2025
  • assembly-analysis-pipeline Public
    EBI-Metagenomics/assembly-analysis-pipeline’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Jan 14, 2025
  • genomes-catalogue-pipeline Public

    MGnify genome analysis pipeline

    EBI-Metagenomics/genomes-catalogue-pipeline’s past year of commit activity
    Python 103 21 7 1 Updated Jan 14, 2025
  • amplicon-pipeline Public
    EBI-Metagenomics/amplicon-pipeline’s past year of commit activity
    Nextflow 5 Apache-2.0 1 0 2 Updated Jan 14, 2025
  • miassembler Public
    EBI-Metagenomics/miassembler’s past year of commit activity
    Nextflow 1 Apache-2.0 0 0 2 Updated Jan 14, 2025
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