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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. GraphMB GraphMB Public

    Python 35 6

  2. nanomotif nanomotif Public

    Nanomotif - a tool for identifying methylated motifs in metagenomic samples

    Python 24 1

  3. ccvae ccvae Public

    Python 2

  4. vaegbin vaegbin Public

    Python 1 1

  5. Fishnchips_basecaller Fishnchips_basecaller Public

    Python

  6. .github .github Public

Repositories

Showing 7 of 7 repositories
  • nanomotif Public

    Nanomotif - a tool for identifying methylated motifs in metagenomic samples

    MicrobialDarkMatter/nanomotif’s past year of commit activity
    Python 24 MIT 1 6 1 Updated Dec 17, 2024
  • MfD-spatial-integration Public
    MicrobialDarkMatter/MfD-spatial-integration’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jun 10, 2024
  • GraphMB Public
    MicrobialDarkMatter/GraphMB’s past year of commit activity
    Python 35 MIT 6 6 0 Updated Nov 20, 2023
  • 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 1 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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