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@sourmash-bio sourmash, for large-scale biological sequence search!

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    34 repositories

    • 2024-benchmark-gather

      Public
      Benchmarking code for various gather implementations
      Jupyter Notebook
      •0•0•0•0•Updated Nov 23, 2024Nov 23, 2024

    • sourmash

      Public
      Quickly search, compare, and analyze genomic and metagenomic data sets.
      rustminhashsketchingkmerhacktoberfesttaxonomic-classificationsourmashtaxonomic-profilingscaled-minhashfracminhash
      Python
      •
      Other
      •79•476•673•60•Updated Nov 21, 2024Nov 21, 2024

    • sourmash_plugin_branchwater

      Public
      fast, multithreaded sourmash operations: search, compare, and gather.
      sourmash
      Python
      •
      GNU Affero General Public License v3.0
      •3•16•86•18•Updated Nov 21, 2024Nov 21, 2024

    • sourmash_plugin_directsketch

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•15•10•Updated Nov 18, 2024Nov 18, 2024

    • wort

      Public
      A database for signatures of public genomic sources
      webservicebioinformaticsminhashbioinformatics-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

    • branchwater

      Public
      Searching large collections of sequencing data with genome-scale queries
      metagenomicssourmash
      HTML
      •
      Other
      •2•7•22•1•Updated Sep 27, 2024Sep 27, 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

    • sourmash_plugin_template

      Public template
      template for building sourmash plugins
      sourmash
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•1•0•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

    • build-ncbi-lineages

      Public
      build NCBI lineages file for sourmash taxonomy
      Python
      •0•0•0•0•Updated Feb 8, 2023Feb 8, 2023

    • sourmash_plugin_avro

      Public
      A sourmash plugin to read and write sketches using Apache Avro.
      Standard ML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Jan 5, 2023Jan 5, 2023

    • parallel-pairwise

      Public
      Brute-force multithreading clustering of sourmash sigs
      Standard ML
      •0•0•0•0•Updated Aug 10, 2022Aug 10, 2022

    • sourmash-examples

      Public
      Example commands for doing sequence analysis with sourmash
      sourmash
      Makefile
      •0•2•16•0•Updated Jul 2, 2022Jul 2, 2022