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@dib-lab

The Lab for Data Intensive Biology

Previously "Genomics, Evolution, and Development Lab" @ Michigan State University
README.md

The Lab for Data Intensive Biology at UC Davis

See http://ivory.idyll.org/lab/

In addition to the pinned repositories within dib-lab, we also work on and help maintain the following software:

sourmash, for rapid large-scale sequence search.

spacegraphcats, for querying large annoying metagenome assembly graphs.

Pinned Loading

  1. khmer khmer Public

    In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

    Python 775 296

  2. charcoal charcoal Public

    Remove contaminated contigs from genomes using k-mers and taxonomies.

    Python 59 1

  3. genome-grist genome-grist Public

    map Illumina metagenomes to genomes!

    Jupyter Notebook 39 6

Repositories

Showing 10 of 175 repositories
  • sourmash_plugin_pangenomics Public

    tools for sourmash-based pangenome analyses

    dib-lab/sourmash_plugin_pangenomics’s past year of commit activity
    Python 1 BSD-3-Clause 1 5 2 Updated Aug 28, 2025
  • genome-grist Public

    map Illumina metagenomes to genomes!

    dib-lab/genome-grist’s past year of commit activity
    Jupyter Notebook 39 6 112 (1 issue needs help) 5 Updated Aug 28, 2025
  • chill-filter Public

    Sample screening software for shotgun sequencing data, using sourmash

    dib-lab/chill-filter’s past year of commit activity
    Python 3 AGPL-3.0 0 7 1 Updated Aug 13, 2025
  • 2025-cami-old-db Public

    Process old CAMI II files into sourmash manysketch & lineage formats

    dib-lab/2025-cami-old-db’s past year of commit activity
    Python 0 0 0 0 Updated Aug 11, 2025
  • q2-sourmash Public

    Qiime2 Sourmash Plugin

    dib-lab/q2-sourmash’s past year of commit activity
    Python 6 BSD-3-Clause 3 2 1 Updated Jul 9, 2025
  • 2022-branchwater-benchmarking Public

    Benchmarking etc code for https://dib-lab.github.io/2022-paper-branchwater-software/

    dib-lab/2022-branchwater-benchmarking’s past year of commit activity
    Jupyter Notebook 2 0 4 4 Updated Jun 24, 2025
  • 2020-paper-sourmash-gather Public

    Here we describe an extension of MinHash that permits accurate compositional analysis of metagenomes with low memory and disk requirements.

    dib-lab/2020-paper-sourmash-gather’s past year of commit activity
    HTML 8 1 27 0 Updated Jun 23, 2025
  • 2022-paper-branchwater-software Public

    Branchwater (MAGsearch) software paper / manubot

    dib-lab/2022-paper-branchwater-software’s past year of commit activity
    HTML 0 0 3 2 Updated Jun 20, 2025
  • farm-notes Public

    notes on the farm cluster

    dib-lab/farm-notes’s past year of commit activity
    16 10 46 4 Updated Feb 26, 2025
  • TheGreatGenotyper Public
    dib-lab/TheGreatGenotyper’s past year of commit activity
    C++ 5 GPL-3.0 0 2 0 Updated Jan 4, 2025
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