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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 789 298

  2. charcoal charcoal Public

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

    Python 60 2

  3. genome-grist genome-grist Public

    map Illumina metagenomes to genomes!

    Jupyter Notebook 38 6

Repositories

Showing 10 of 177 repositories
  • 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 Apr 16, 2026
  • 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 2 Updated Apr 1, 2026
  • screed Public

    a simple read-only sequence database, designed for short reads

    dib-lab/screed’s past year of commit activity
    Python 65 32 10 5 Updated Mar 27, 2026
  • 2025-workflow-core99 Public

    Workflow for pig core99 microbiome

    dib-lab/2025-workflow-core99’s past year of commit activity
    Jupyter Notebook 1 BSD-3-Clause 0 0 1 Updated Mar 24, 2026
  • genome-grist Public

    map Illumina metagenomes to genomes!

    dib-lab/genome-grist’s past year of commit activity
    Jupyter Notebook 38 6 117 (1 issue needs help) 10 Updated Jan 22, 2026
  • 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 6 3 Updated Jan 12, 2026
  • sourmash-midgie-raker Public

    Utilities and workflows for examining (metagenome) binning results

    dib-lab/sourmash-midgie-raker’s past year of commit activity
    Jupyter Notebook 1 BSD-3-Clause 0 0 2 Updated Nov 26, 2025
  • pybbhash Public

    A Python wrapper for the bbhash library for Minimal Perfect Hashing

    dib-lab/pybbhash’s past year of commit activity
    C++ 19 5 6 0 Updated Oct 26, 2025
  • kmerDecoder Public

    Extract kmers, skipmers, minimizers.

    dib-lab/kmerDecoder’s past year of commit activity
    C++ 10 3 15 0 Updated Oct 24, 2025
  • dib-lab Public

    Issue tracker and Web site for the Lab for Data Intensive Biology at UC Davis.

    dib-lab/dib-lab’s past year of commit activity
    Python 8 20 44 2 Updated Oct 13, 2025
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