Repositories list

• branchwater

  Public
  Searching large collections of sequencing data with genome-scale queries

  metagenomicssourmash

  HTML

  •

  Other

  •2•10•22•0•Updated Jan 24, 2025Jan 24, 2025

• 2025-sourmash-eukaryotic-databases

  Public
  Build infrastructure for creating sourmash databases from NCBI for all eukaryotes

  Python

  •

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

  •0•0•0•0•Updated Jan 22, 2025Jan 22, 2025

• sourmash

  Public
  Quickly search, compare, and analyze genomic and metagenomic data sets.

  rustminhashsketching+ 9kmerhacktoberfesttaxonomic-classificationsourmashtaxonomic-profilingscaled-minhashfracminhash+ 2

  Python

  •

  Other

  •80•484•692•59•Updated Jan 21, 2025Jan 21, 2025

• sourmash_plugin_branchwater

  Public
  fast, multithreaded sourmash operations: search, compare, and gather.

  sourmash

  Python

  •

  GNU Affero General Public License v3.0

  •4•21•97•17•Updated Jan 20, 2025Jan 20, 2025

• sourmash_plugin_directsketch

  Public
  Rust

  •

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

  •1•3•24•3•Updated Jan 20, 2025Jan 20, 2025

• sourmash_plugin_template

  Public template
  template for building sourmash plugins

  sourmash

  Python

  •

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

  •0•2•1•0•Updated Jan 19, 2025Jan 19, 2025

• 2024-ictv-challenge-sourmash

  Public
  Python

  •0•0•0•0•Updated Dec 31, 2024Dec 31, 2024

• sourmash_plugin_tables

  Public
  Tables is a python-based sourmash plugin to convert the standard output files from base sourmash into an OTU format. See README for more information.

  Python

  •

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

  •0•0•1•0•Updated Dec 19, 2024Dec 19, 2024

• 2024-sketch-animal-genomes

  Public
  Sketch human, mouse, cow, chick, and other animal genomes.

  Python

  •0•0•0•0•Updated Dec 14, 2024Dec 14, 2024

• 2024-benchmark-gather

  Public
  Benchmarking code for various gather implementations

  Jupyter Notebook

  •0•0•0•0•Updated Nov 23, 2024Nov 23, 2024

• wort

  Public
  A database for signatures of public genomic sources

  webservicebioinformaticsminhash+ 2bioinformatics-databasessourmash

  Python

  •

  Other

  •2•18•22•1•Updated Nov 17, 2024Nov 17, 2024

• sourmash.bio

  Public
  Dockerfile

  •0•0•0•0•Updated Oct 6, 2024Oct 6, 2024

• sourmash_plugin_betterplot

  Public
  Improved plotting/viz and cluster examination for sourmash

  sourmash

  Python

  •

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

  •0•1•20•1•Updated Sep 18, 2024Sep 18, 2024

• sourmash_plugin_hashannot

  Public
  sourmash utilities for annotating hashes with genomic information

  Python

  •

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

  •0•0•0•1•Updated Aug 30, 2024Aug 30, 2024

• database-releases

  Public
  Build infrastructure for official sourmash database releases

  Python

  •

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

  •1•1•2•3•Updated Aug 14, 2024Aug 14, 2024

• sourmash_plugin_venn

  Public archive
  venn diagrams for sourmash sketches! (DEPRECATED)

  sourmash

  Python

  •

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

  •0•1•0•0•Updated Aug 11, 2024Aug 11, 2024

• sourmash_plugin_containment_search

  Public
  An improved `search --containment` for sourmash

  Python

  •

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

  •0•2•6•0•Updated Jul 30, 2024Jul 30, 2024

• sourmash_utils

  Public
  Python utilities for sourmash plugins and scripts

  Python

  •0•0•2•1•Updated Jun 18, 2024Jun 18, 2024

• 2024-benchmark-branchwater-plugin

  Public
  Some simple benchmarking code for sourmash_plugin_branchwater

  Shell

  •

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

  •0•0•0•0•Updated Feb 18, 2024Feb 18, 2024

• mastiff

  Public archive
  Rust

  •

  Other

  •0•16•0•0•Updated Jan 21, 2024Jan 21, 2024

• .github

  Public
  0•0•1•0•Updated Jan 21, 2024Jan 21, 2024

• branchwater-old

  Public archive
  Code and workflows for large-scale genomic search of e.g. the Sequence Read Archive

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

  •0•8•0•1•Updated Jan 21, 2024Jan 21, 2024

• 2023-branchwater-validate

  Public
  Validation and testing for sourmash branchwater

  sourmash

  Jupyter Notebook

  •0•1•0•0•Updated Sep 1, 2023Sep 1, 2023

• sra_search

  Public
  Rust

  •

  GNU Affero General Public License v3.0

  •0•0•2•2•Updated Aug 28, 2023Aug 28, 2023

• sourmash_plugin_randsampling

  Public
  kmers extraction based on weighted-random-sampling

  Python

  •

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

  •1•1•1•0•Updated Aug 12, 2023Aug 12, 2023

• sourmash-mixers

  Public
  A meta-package to install a number of sourmash plugins!

  sourmash

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

  •0•4•5•0•Updated Aug 5, 2023Aug 5, 2023

• sourmash_plugin_sketchall

  Public
  Sketch many files at once

  sourmash

  Python

  •

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

  •0•2•1•0•Updated Aug 3, 2023Aug 3, 2023

• sourmash_plugin_load_urls

  Public
  sourmash plugin to load files from URLs with fsspec.

  Standard ML

  •

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

  •0•1•0•0•Updated Jul 27, 2023Jul 27, 2023

• databases

  Public
  Build sourmash databases for genbank.

  sourmash

  Python

  •1•12•3•1•Updated May 4, 2023May 4, 2023

• 2022-search-sra-with-mastiff

  Public
  Tools and utilities for making use of mastiff

  Jupyter Notebook

  •

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

  •1•12•3•0•Updated Mar 10, 2023Mar 10, 2023