Repositories list

• chill-filter

  Public

  dib-lab/chill-filter’s past year of commit activity
  Sample screening software for shotgun sequencing data, using sourmash

  Python

  •

  GNU Affero General Public License v3.0

  •00 forks•33 stars•77 issues•22 pull requests•Updated Apr 1, 2026Apr 1, 2026

• screed

  Public

  dib-lab/screed’s past year of commit activity
  a simple read-only sequence database, designed for short reads

  Python

  •3232 forks•6565 stars•1010 issues•55 pull requests•Updated Mar 27, 2026Mar 27, 2026

• 2025-workflow-core99

  Public

  dib-lab/2025-workflow-core99’s past year of commit activity
  Workflow for pig core99 microbiome

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•11 pull request•Updated Mar 24, 2026Mar 24, 2026

• q2-sourmash

  Public

  dib-lab/q2-sourmash’s past year of commit activity
  Qiime2 Sourmash Plugin

  sourmash

  sourmash

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •33 forks•66 stars•22 issues•11 pull request•Updated Jan 27, 2026Jan 27, 2026

• genome-grist

  Public

  dib-lab/genome-grist’s past year of commit activity
  map Illumina metagenomes to genomes!

  hacktoberfestsourmash

  hacktoberfestsourmash

  Jupyter Notebook

  •

  Other

  •66 forks•3838 stars•117117 issues•1010 pull requests•Updated Jan 22, 2026Jan 22, 2026

• sourmash_plugin_pangenomics

  Public

  dib-lab/sourmash_plugin_pangenomics’s past year of commit activity
  tools for sourmash-based pangenome analyses

  sourmash

  sourmash

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •11 fork•11 star•66 issues•33 pull requests•Updated Jan 12, 2026Jan 12, 2026

• sourmash-midgie-raker

  Public

  dib-lab/sourmash-midgie-raker’s past year of commit activity
  Utilities and workflows for examining (metagenome) binning results

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•11 star•00 issues•22 pull requests•Updated Nov 26, 2025Nov 26, 2025

• pybbhash

  Public

  dib-lab/pybbhash’s past year of commit activity
  A Python wrapper for the bbhash library for Minimal Perfect Hashing

  C++

  •

  Other

  •55 forks•1919 stars•66 issues•00 pull requests•Updated Oct 26, 2025Oct 26, 2025

• kmerDecoder

  Public

  dib-lab/kmerDecoder’s past year of commit activity
  Extract kmers, skipmers, minimizers.

  kmersskipmersskip-mers+ 1

  kmersskipmersskip-mersminimizers

  C++

  •33 forks•1010 stars•1515 issues•00 pull requests•Updated Oct 24, 2025Oct 24, 2025

• dib-lab

  Public

  dib-lab/dib-lab’s past year of commit activity
  Issue tracker and Web site for the Lab for Data Intensive Biology at UC Davis.

  Python

  •2020 forks•88 stars•4444 issues•22 pull requests•Updated Oct 13, 2025Oct 13, 2025

• 2022-branchwater-benchmarking

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

  sourmash

  sourmash

  Jupyter Notebook

  •00 forks•22 stars•44 issues•44 pull requests•Updated Sep 17, 2025Sep 17, 2025

• 2025-cami-old-db

  Public
  Process old CAMI II files into sourmash manysketch & lineage formats

  Python

  •00 forks•11 star•00 issues•00 pull requests•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

  sourmash

  HTML

  •

  Other

  •11 fork•88 stars•2727 issues•00 pull requests•Updated Jun 23, 2025Jun 23, 2025

• 2022-paper-branchwater-software

  Public
  Branchwater (MAGsearch) software paper / manubot

  HTML

  •

  Other

  •00 forks•00 stars•33 issues•22 pull requests•Updated Jun 20, 2025Jun 20, 2025

• farm-notes

  Public
  notes on the farm cluster

  1111 forks•1616 stars•4646 issues•44 pull requests•Updated Feb 26, 2025Feb 26, 2025

• TheGreatGenotyper

  Public
  C++

  •

  GNU General Public License v3.0

  •00 forks•1010 stars•22 issues•00 pull requests•Updated Jan 4, 2025Jan 4, 2025

• 2024-december-hackathon

  Public
  Organizing repo for 2024 december hackathon (look at issues)

  00 forks•00 stars•22 issues•00 pull requests•Updated Dec 13, 2024Dec 13, 2024

• assembly-exercise

  Public
  Shotgun sequencing of text, in CGI script form

  Python

  •77 forks•77 stars•00 issues•00 pull requests•Updated Sep 24, 2024Sep 24, 2024

• kSpider

  Public
  A simple yet powerful sequence clustering tool.

  clusteringdnaprotein+ 2

  clusteringdnaproteindna-sequencesskipmers

  C++

  •

  MIT License

  •11 fork•88 stars•1818 issues•11 pull request•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

  •11 fork•11 star•55 issues•00 pull requests•Updated Aug 14, 2024Aug 14, 2024

• TheGreatGenotyper_benchmark

  Public
  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 13, 2024Jul 13, 2024

• TheGreatGenotyper_usecases

  Public
  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 13, 2024Jul 13, 2024

• 2020-NSURP

  Public
  Python

  •11 fork•11 star•11 issue•00 pull requests•Updated Jun 22, 2024Jun 22, 2024

• sourmash-slainte

  Public template
  Project template for sourmash-based characterization of genomes and metagenomes

  sourmash

  sourmash

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•11 star•66 issues•33 pull requests•Updated May 16, 2024May 16, 2024

• 2022-database-covers

  Public
  Python

  •22 forks•11 star•22 issues•11 pull request•Updated May 15, 2024May 15, 2024

• sourmash_plugin_colorcompare

  Public
  Add colors representing categories in sourmash compare plots.

  sourmash

  sourmash

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 7, 2024Mar 7, 2024

• khmer

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

  pythonbioinformaticsbloom-filter+ 4

  pythonbioinformaticsbloom-filterdnacount-min-sketchk-mergraph-traversal

  Python

  •

  Other

  •299299 forks•786786 stars•309309 issues•4444 pull requests•Updated Feb 17, 2024Feb 17, 2024

• dib_rotation

  Public
  Metagenomics DIB-lab rotation project

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •99 forks•33 stars•2424 issues•22 pull requests•Updated Feb 9, 2024Feb 9, 2024

• Cattle_Structural_Variant_Benchmark

  Public
  Python

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 15, 2024Jan 15, 2024

• Cattle_SV_Catalog

  Public
  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 12, 2024Jan 12, 2024