Repositories list

• genome-grist

  Public
  map Illumina metagenomes to genomes!

  hacktoberfestsourmash

  Jupyter Notebook

  •

  Other

  •6•38•106•14•Updated Mar 14, 2025Mar 14, 2025

• farm-notes

  Public
  notes on the farm cluster

  9•16•44•4•Updated Feb 26, 2025Feb 26, 2025

• TheGreatGenotyper

  Public
  C++

  •

  GNU General Public License v3.0

  •0•4•2•0•Updated Jan 4, 2025Jan 4, 2025

• chill-filter

  Public
  Sample screening software for shotgun sequencing data, using sourmash

  Python

  •

  GNU Affero General Public License v3.0

  •0•2•6•1•Updated Dec 30, 2024Dec 30, 2024

• q2-sourmash

  Public
  Qiime2 Sourmash Plugin

  sourmash

  Python

  •

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

  •4•6•2•1•Updated Dec 23, 2024Dec 23, 2024

• 2024-december-hackathon

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

  0•0•2•0•Updated Dec 13, 2024Dec 13, 2024

• 2022-branchwater-benchmarking

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

  sourmash

  Jupyter Notebook

  •0•2•4•3•Updated Oct 16, 2024Oct 16, 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.

  clusteringdnaprotein+ 2dna-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_plugin_pangenomics

  Public
  tools for sourmash-based pangenome analyses

  sourmash

  Python

  •

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

  •1•1•5•0•Updated Jun 12, 2024Jun 12, 2024

• kmerDecoder

  Public
  Extract kmers, skipmers, minimizers.

  kmersskipmersskip-mers+ 1minimizers

  C++

  •3•10•15•0•Updated May 24, 2024May 24, 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

  bioinformaticsbloom-filterdna+ 4count-min-sketchk-mergraph-traversalpython

  Python

  •

  Other

  •295•762•309•44•Updated Feb 17, 2024Feb 17, 2024

• dib_rotation

  Public
  Metagenomics DIB-lab rotation project

  Python

  •

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

  •8•3•24•2•Updated Feb 9, 2024Feb 9, 2024

• screed

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

  Python

  •34•66•9•1•Updated Feb 1, 2024Feb 1, 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

• 2021-paper-metapangenomes

  Public
  HTML

  •

  Other

  •2•1•7•1•Updated Dec 22, 2023Dec 22, 2023

• charcoal

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

  bioinformaticsmetagenomicsk-mer+ 1sourmash

  Python

  •

  Other

  •1•56•119•6•Updated Nov 3, 2023Nov 3, 2023

• 2018-ncbi-lineages

  Public
  Extract lineage CSVs from NCBI for use with sourmash lca.

  Python

  •

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

  •6•28•0•1•Updated Oct 4, 2023Oct 4, 2023

• kProcessor

  Public
  kProcessor: kmers processing framework.

  C++

  •

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

  •1•11•55•3•Updated Oct 1, 2023Oct 1, 2023

• MQF

  Public
  C++

  •

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

  •0•12•6•0•Updated Oct 1, 2023Oct 1, 2023

• dib-lab

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

  Python

  •19•7•44•2•Updated Oct 1, 2023Oct 1, 2023

• dammit

  Public
  just annotate it, dammit!

  bioinformaticstranscriptomicsannotation

  Python

  •

  Other

  •28•91•67•12•Updated Aug 22, 2023Aug 22, 2023