{"id":13958718,"url":"https://github.com/sourmash-bio/sourmash","last_synced_at":"2025-10-21T20:03:58.800Z","repository":{"id":36993094,"uuid":"55858065","full_name":"sourmash-bio/sourmash","owner":"sourmash-bio","description":"Quickly search, compare, and analyze genomic and metagenomic data 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sourmash\n\nQuickly search, compare, and analyze genomic and metagenomic data sets.\n\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n\u003ca href=\"https://github.com/sourmash-bio/sourmash/blob/latest/LICENSE\"\u003e\u003cimg alt=\"License: 3-Clause BSD\" src=\"https://img.shields.io/badge/License-BSD%203--Clause-blue.svg\"\u003e\u003c/a\u003e\n[![Documentation](https://readthedocs.org/projects/sourmash/badge/?version=latest)](http://sourmash.readthedocs.io/en/latest/)\n[![Gitter](https://badges.gitter.im/sourmash-bio/community.svg)](https://gitter.im/sourmash-bio/community?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge)\n\n[![DOI](https://joss.theoj.org/papers/10.21105/joss.06830/status.svg)](https://doi.org/10.21105/joss.06830)\n[![pyOpenSci](https://tinyurl.com/y22nb8up)](https://github.com/pyOpenSci/software-submission/issues/129)\n\n[![Bioconda install](https://img.shields.io/conda/dn/bioconda/sourmash.svg?style=flag\u0026label=Bioconda)](https://anaconda.org/bioconda/sourmash)\n\u003ca href=\"https://pypi.org/project/sourmash/\"\u003e\u003cimg alt=\"PyPI\" src=\"https://badge.fury.io/py/sourmash.svg\"\u003e\u003c/a\u003e\n[![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/sourmash-minimal.svg)](https://anaconda.org/conda-forge/sourmash-minimal)\n[![Debian Testing](https://badges.debian.net/badges/debian/testing/sourmash/version.svg)](https://packages.debian.org/testing/sourmash) [![Debian Unstable](https://badges.debian.net/badges/debian/unstable/sourmash/version.svg)](https://packages.debian.org/unstable/sourmash)\n\n![Python 3.11](https://img.shields.io/badge/python-3.11-blue.svg)\n![Python 3.12](https://img.shields.io/badge/python-3.12-blue.svg)\n![Python 3.13](https://img.shields.io/badge/python-3.13-blue.svg)\n[![Build Status](https://github.com/sourmash-bio/sourmash/workflows/Python%20tests/badge.svg)](https://github.com/sourmash-bio/sourmash/actions/)\n[![codecov](https://codecov.io/gh/sourmash-bio/sourmash/branch/latest/graph/badge.svg)](https://codecov.io/gh/sourmash-bio/sourmash)\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/sourmash-bio/sourmash/latest/doc/_static/logo.png\" height=\"256\" /\u003e\u003c/p\u003e\n\nUsage:\n\n    sourmash sketch dna *.fq.gz\n    sourmash compare *.sig -o distances.cmp -k 31\n    sourmash plot distances.cmp\n\nsourmash 1.0 is [published on JOSS](https://doi.org/10.21105/joss.06830); please cite that paper if you use sourmash (`doi: 10.21105/joss.06830`):.\n\nThe latest major release is sourmash v4, which has several\ncommand-line and Python incompatibilities with previous\nversions. Please\n[visit our migration guide](https://sourmash.readthedocs.io/en/latest/support.html#migrating-from-sourmash-v3-x-to-sourmash-4-x)\nto upgrade!\n\n----\n\nsourmash is a k-mer analysis multitool, and we aim to provide stable, robust programmatic and command-line APIs for a variety of sequence comparisons. Some of our special sauce includes:\n- `FracMinHash` sketching, which enables accurate comparisons (including ANI) between data sets of different sizes\n- `sourmash gather`, a combinatorial k-mer approach for more accurate metagenomic profiling\n\nPlease see the [sourmash publications](https://sourmash.readthedocs.io/en/latest/publications.html#sourmash-fundamentals) for details.\n\nThe name is a riff off of [Mash](https://github.com/marbl/Mash),\ncombined with @ctb's love of whiskey.\n([Sour mash](https://en.wikipedia.org/wiki/Sour_mash) is used in\nmaking whiskey.)\n\nMaintainers: [C. Titus Brown](mailto:titus@idyll.org) ([@ctb](http://github.com/ctb)), [Luiz C. Irber, Jr](mailto:luiz@sourmash.bio) ([@luizirber](http://github.com/luizirber)), and [N. Tessa Pierce-Ward](mailto:tessa@sourmash.bio) ([@bluegenes](http://github.com/bluegenes)).\n\nsourmash was initially developed by the\n[Lab for Data-Intensive Biology](http://ivory.idyll.org/lab/) at the\n[UC Davis School of Veterinary Medicine](http://www.vetmed.ucdavis.edu),\nand now includes contributions from the global research and developer\ncommunity.\n\n## Installation\n\nWe recommend using conda-forge to install sourmash:\n\n```\nconda install -c conda-forge sourmash-minimal\n```\nThis will install the latest stable version of sourmash 4.\n\nYou can also use pip to install sourmash:\n\n```\npip install sourmash\n```\n\nA quickstart tutorial [is available](https://sourmash.readthedocs.io/en/latest/tutorials.html).\n\n### Requirements\n\nsourmash runs under Python 3.11 and later on Windows, Mac OS X, and\nLinux.  The base requirements are screed, cffi, numpy, matplotlib, and\nscipy.  Conda will install everything necessary, and is\nour recommended installation method (see below).\n\n### Installation with conda\n\nconda-forge is a community maintained channel for the\n[conda](http://conda.pydata.org/docs/intro.html) package manager.\n[installing conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/),\nyou can install sourmash by running:\n\n```bash\n$ conda create -n sourmash_env -c conda-forge sourmash-minimal\n$ conda activate sourmash_env\n$ sourmash --help\n```\n\nwhich will install\n[the latest released version](https://github.com/sourmash-bio/sourmash/releases).\n\n## Support\n\nFor questions, please open an issue [on Github](https://github.com/sourmash-bio/sourmash/issues), or ask in our [chat](https://gitter.im/sourmash-bio/community?utm_source=share-link\u0026utm_medium=link\u0026utm_campaign=share-link).\n\n## Development\n\nDevelopment happens on github at\n[sourmash-bio/sourmash](https://github.com/sourmash-bio/sourmash).\n\nsourmash is developed in Python and Rust, and you will need a Rust\nenvironment to build it; see [the developer notes](doc/developer.md)\nfor our suggested development setup.\n\nAfter installation, `sourmash` is the main command-line entry point;\nrun it with `python -m sourmash`, or do `pip install -e /path/to/repo` to\ndo a developer install in a virtual environment.\n\nThe `sourmash/` directory contains the Python library and command-line interface code.\n\nThe `src/core/` directory contains the Rust library implementing core\nfunctionality.\n\nTests require py.test and can be run with `make test`.\n\nPlease see [the developer notes](doc/developer.md) for more information\non getting set up with a development environment.\n\nCTB\nJan 2024\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsourmash-bio%2Fsourmash","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsourmash-bio%2Fsourmash","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsourmash-bio%2Fsourmash/lists"}