8000 sourmash-bio repositories · GitHub

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sourmash, for large-scale biological sequence search!

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40 repositories

branchwater
Public
Searching large collections of sequencing data with genome-scale queries
metagenomics sourmash
Rust
•
Other
•3•11•27•4•Updated Feb 25, 2025Feb 25, 2025
2025-sourmash-ncbi-viral-databases
Public
Build infrastructure for creating sourmash databases from NCBI for all viruses
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Feb 25, 2025Feb 25, 2025
sourmash
Public
Quickly search, compare, and analyze genomic and metagenomic data sets.
rust minhash sketching kmer hacktoberfest taxonomic-classification sourmash taxonomic-profiling scaled-minhash fracminhash
Python
•
Other
•80•488•713•68•Updated Feb 24, 2025Feb 24, 2025
sourmash_plugin_branchwater
Public
fast, multithreaded sourmash operations: search, compare, and gather.
sourmash
Python
•
GNU Affero General Public License v3.0
•5•21•102•19•Updated Feb 24, 2025Feb 24, 2025
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 Feb 24, 2025Feb 24, 2025
sourmash_plugin_directsketch
Public
Rust
•
BSD 3-Clause "New" or "Revised" License
•1•3•23•6•Updated Feb 24, 2025Feb 24, 2025
sourmash_plugin_betterplot
Public
Improved plotting/viz and cluster examination for sourmash
sourmash
Python
•
BSD 3-Clause "New" or "Revised" License
•0•2•22•1•Updated Feb 15, 2025Feb 15, 2025
wort
Public
A database for signatures of public genomic sources
webservice bioinformatics minhash bioinformatics-databases sourmash
Python
•
Other
•2•18•23•2•Updated Feb 8, 2025Feb 8, 2025
2025-sourmash-databases-doc-template
Public
Template structure for building new sourmash database doc files
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•1•0•Updated Feb 1, 2025Feb 1, 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_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
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
sourmash.bio
Public
Dockerfile
•0•0•0•0•Updated Oct 6, 2024Oct 6, 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
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BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Jul 27, 2023Jul 27, 2023

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