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@MicrobialDarkMatter

Microbial Dark Matter @ AAU

README.md

Microbial DarkMatter project

This repository includes projects and papers created in the context of the Microbial Dark Matter project (2021-2023)

More info can be found on the project webpage: https://darkmatter.aau.dk

Software projects

Release as packages

  • GraphMB: Metagenomics binner using assembly graph and graph convolutional networks

Experiments

  • VaeG-Bin: Metagenomics binner using GNNs and single copy genes (incorporated into GraphMB)
  • CCVAE: Metagenomics binner using a connectivity-constrained loss function on an VAE (no GNN, also incorporated into GraphMB)
  • Fishnchips: ONT basecaller

Papers and manuscripts

  • metagenomics-genome-recovery: Background and state-of-the-art of metagenomics for bioinformatics, made in 2021
  • assembly graph bin: GraphMB paper for Bioinformatics (published in 2022)

Posters

Popular repositories Loading

  1. nanomotif nanomotif Public

    Nanomotif - a tool for identifying methylated motifs in metagenomic samples

    Python 38 2

  2. GraphMB GraphMB Public

    Python 36 8

  3. ccvae ccvae Public

    Python 2

  4. EcoGP EcoGP Public

    Python 2

  5. vaegbin vaegbin Public

    Python 1

  6. Fishnchips_basecaller Fishnchips_basecaller Public

    Python

Repositories

Showing 9 of 9 repositories
  • GraphMB Public
    MicrobialDarkMatter/GraphMB's past year of commit activity
    Python 36 MIT 8 6 0 Updated Aug 7, 2026
  • EcoGP Public
    MicrobialDarkMatter/EcoGP's past year of commit activity
    Python 2 MIT 0 0 0 Updated Apr 17, 2026
  • nanomotif Public

    Nanomotif - a tool for identifying methylated motifs in metagenomic samples

    MicrobialDarkMatter/nanomotif's past year of commit activity
    Python 38 MIT 2 11 1 Updated Apr 10, 2026
  • Biogeography Public

    Modeling of Species

    MicrobialDarkMatter/Biogeography's past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 6, 2026
  • MfD-spatial-integration Public
    MicrobialDarkMatter/MfD-spatial-integration's past year of commit activity
    Python 0 MIT 0 0 0 Updated Aug 6, 2025
  • ccvae Public
    MicrobialDarkMatter/ccvae's past year of commit activity
    Python 2 0 0 0 Updated Jul 12, 2023
  • vaegbin Public
    MicrobialDarkMatter/vaegbin's past year of commit activity
    Python 1 0 0 0 Updated May 18, 2023
  • .github Public
    MicrobialDarkMatter/.github's past year of commit activity
    0 0 0 0 Updated Jan 27, 2023
  • Fishnchips_basecaller Public
    MicrobialDarkMatter/Fishnchips_basecaller's past year of commit activity
    Python 0 0 0 0 Updated Mar 29, 2021

People

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