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    177 repositories

    • 2025-workflow-core99

      Public
      Workflow for pig core99 microbiome
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Feb 22, 2026Feb 22, 2026

    • screed

      Public
      a simple read-only sequence database, designed for short reads
      Python
      •32•65•9•4•Updated Feb 16, 2026Feb 16, 2026

    • q2-sourmash

      Public
      Qiime2 Sourmash Plugin
      sourmash
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•6•2•1•Updated Jan 27, 2026Jan 27, 2026

    • genome-grist

      Public
      map Illumina metagenomes to genomes!
      hacktoberfestsourmash
      Jupyter Notebook
      •
      Other
      •6•38•117•10•Updated Jan 22, 2026Jan 22, 2026

    • sourmash_plugin_pangenomics

      Public
      tools for sourmash-based pangenome analyses
      sourmash
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•6•3•Updated Jan 12, 2026Jan 12, 2026

    • sourmash-midgie-raker

      Public
      Utilities and workflows for examining (metagenome) binning results
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•2•Updated Nov 26, 2025Nov 26, 2025

    • pybbhash

      Public
      A Python wrapper for the bbhash library for Minimal Perfect Hashing
      C++
      •
      Other
      •5•19•6•0•Updated Oct 26, 2025Oct 26, 2025

    • kmerDecoder

      Public
      Extract kmers, skipmers, minimizers.
      kmersskipmersskip-mersminimizers
      C++
      •3•10•15•0•Updated Oct 24, 2025Oct 24, 2025

    • dib-lab

      Public
      Issue tracker and Web site for the Lab for Data Intensive Biology at UC Davis.
      Python
      •20•8•44•2•Updated Oct 13, 2025Oct 13, 2025

    • 2022-branchwater-benchmarking

      Public
      Benchmarking etc code for https://dib-lab.github.io/2022-paper-branchwater-software/
      sourmash
      Jupyter Notebook
      •0•2•4•4•Updated Sep 17, 2025Sep 17, 2025

    • chill-filter

      Public
      Sample screening software for shotgun sequencing data, using sourmash
      Python
      •
      GNU Affero General Public License v3.0
      •0•3•7•1•Updated Aug 13, 2025Aug 13, 2025

    • 2025-cami-old-db

      Public
      Process old CAMI II files into sourmash manysketch & lineage formats
      Python
      •0•1•0•0•Updated Aug 11, 2025Aug 11, 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.
      sourmash
      HTML
      •
      Other
      •1•8•27•0•Updated Jun 23, 2025Jun 23, 2025

    • 2022-paper-branchwater-software

      Public
      Branchwater (MAGsearch) software paper / manubot
      HTML
      •
      Other
      •0•0•3•2•Updated Jun 20, 2025Jun 20, 2025

    • farm-notes

      Public
      notes on the farm cluster
      11•16•46•4•Updated Feb 26, 2025Feb 26, 2025

    • TheGreatGenotyper

      Public
      C++
      •
      GNU General Public License v3.0
      •0•10•2•0•Updated Jan 4, 2025Jan 4, 2025

    • 2024-december-hackathon

      Public
      Organizing repo for 2024 december hackathon (look at issues)
      0•0•2•0•Updated Dec 13, 2024Dec 13, 2024

    • assembly-exercise

      Public
      Shotgun sequencing of text, in CGI script form
      Python
      •7•7•0•0•Updated Sep 24, 2024Sep 24, 2024

    • kSpider

      Public
      A simple yet powerful sequence clustering tool.
      clusteringdnaproteindna-sequencesskipmers
      C++
      •
      MIT License
      •1•8•18•1•Updated Sep 3, 2024Sep 3, 2024

    • portable-snakemake-workflows

      Public
      A small, fast, robust workflows using snakemake!
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•5•0•Updated Aug 14, 2024Aug 14, 2024

    • TheGreatGenotyper_benchmark

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 13, 2024Jul 13, 2024

    • TheGreatGenotyper_usecases

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 13, 2024Jul 13, 2024

    • 2020-NSURP

      Public
      Python
      •1•1•1•0•Updated Jun 22, 2024Jun 22, 2024

    • sourmash-slainte

      Public template
      Project template for sourmash-based characterization of genomes and metagenomes
      sourmash
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•6•3•Updated May 16, 2024May 16, 2024

    • 2022-database-covers

      Public
      Python
      •2•1•2•1•Updated May 15, 2024May 15, 2024

    • sourmash_plugin_colorcompare

      Public
      Add colors representing categories in sourmash compare plots.
      sourmash
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Mar 7, 2024Mar 7, 2024

    • khmer

      Public
      In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
      pythonbioinformaticsbloom-filterdnacount-min-sketchk-mergraph-traversal
      Python
      •
      Other
      •298•785•309•44•Updated Feb 17, 2024Feb 17, 2024

    • dib_rotation

      Public
      Metagenomics DIB-lab rotation project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •9•3•24•2•Updated Feb 9, 2024Feb 9, 2024

    • Cattle_Structural_Variant_Benchmark

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 15, 2024Jan 15, 2024

    • Cattle_SV_Catalog

      Public
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 12, 2024Jan 12, 2024