| Name | sourmash JSON |
| Version |
4.8.8
JSON |
| download |
| home_page | None |
| Summary | tools for comparing biological sequences with k-mer sketches |
| upload_time | 2024-04-09 23:09:22 |
| maintainer | None |
| docs_url | None |
| author | Luiz Irber, N. Tessa Pierce-Ward, Mohamed Abuelanin, Harriet Alexander, Abhishek Anant, Keya Barve, Colton Baumler, Olga Botvinnik, Phillip Brooks, Peter Cock, Daniel Dsouza, Jade Gardner, Laurent Gautier, Tim Head, Mahmudur Rahman Hera, Hannah Eve Houts, Lisa K. Johnson, Fabian Klötzl, David Koslicki, Katrin Leinweber, Marisa Lim, Ricky Lim, Bradley Nelson, Ivan Ogasawara, Taylor Reiter, Camille Scott, Andreas Sjödin, Connor T. Skennerton, Jason Stajich, Daniel Standage, S. Joshua Swamidass, Connor Tiffany, Pranathi Vemuri, Erik Young, Nick H, C. Titus Brown |
| requires_python | >=3.10 |
| license | BSD-3-Clause |
| keywords |
minhash
bioinformatics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
[](https://www.repostatus.org/#active)
<a href="https://github.com/sourmash-bio/sourmash/blob/latest/LICENSE"><img alt="License: 3-Clause BSD" src="https://img.shields.io/badge/License-BSD%203--Clause-blue.svg"></a>
[](http://sourmash.readthedocs.io/en/latest/)
[](https://gitter.im/sourmash-bio/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
[](http://joss.theoj.org/papers/10.21105/joss.00027)
[](https://github.com/pyOpenSci/software-submission/issues/129)
[](https://anaconda.org/bioconda/sourmash)
<a href="https://pypi.org/project/sourmash/"><img alt="PyPI" src="https://badge.fury.io/py/sourmash.svg"></a>
[](https://anaconda.org/conda-forge/sourmash-minimal)
[](https://github.com/sourmash-bio/sourmash/actions/)
[](https://codecov.io/gh/sourmash-bio/sourmash)
<p align="center"><img src="https://raw.githubusercontent.com/sourmash-bio/sourmash/latest/doc/_static/logo.png" height="256" /></p>
Usage:
sourmash sketch dna *.fq.gz
sourmash compare *.sig -o distances.cmp -k 31
sourmash plot distances.cmp
sourmash 1.0 is [published on JOSS](https://doi.org/10.21105/joss.00027); please cite that paper if you use sourmash (`doi: 10.21105/joss.00027`):.
The latest major release is sourmash v4, which has several
command-line and Python incompatibilities with previous
versions. Please
[visit our migration guide](https://sourmash.readthedocs.io/en/latest/support.html#migrating-from-sourmash-v3-x-to-sourmash-4-x)
to upgrade!
----
sourmash 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:
- `FracMinHash` sketching, which enables accurate comparisons (including ANI) between data sets of different sizes
- `sourmash gather`, a combinatorial k-mer approach for more accurate metagenomic profiling
Please see the [sourmash publications](https://sourmash.readthedocs.io/en/latest/publications.html#sourmash-fundamentals) for details.
The name is a riff off of [Mash](https://github.com/marbl/Mash),
combined with @ctb's love of whiskey.
([Sour mash](https://en.wikipedia.org/wiki/Sour_mash) is used in
making whiskey.)
Maintainers: [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)).
sourmash was initially developed by the
[Lab for Data-Intensive Biology](http://ivory.idyll.org/lab/) at the
[UC Davis School of Veterinary Medicine](http://www.vetmed.ucdavis.edu),
and now includes contributions from the global research and developer
community.
## Installation
We recommend using conda-forge to install sourmash:
```
conda install -c conda-forge sourmash-minimal
```
This will install the latest stable version of sourmash 4.
You can also use pip to install sourmash:
```
pip install sourmash
```
A quickstart tutorial [is available](https://sourmash.readthedocs.io/en/latest/tutorials.html).
### Requirements
sourmash runs under Python 3.10 and later on Windows, Mac OS X, and
Linux. The base requirements are screed, cffi, numpy, matplotlib, and
scipy. Conda will install everything necessary, and is
our recommended installation method (see below).
### Installation with conda
conda-forge is a community maintained channel for the
[conda](http://conda.pydata.org/docs/intro.html) package manager.
[installing conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/),
you can install sourmash by running:
```bash
$ conda create -n sourmash_env -c conda-forge sourmash-minimal
$ conda activate sourmash_env
$ sourmash --help
```
which will install
[the latest released version](https://github.com/sourmash-bio/sourmash/releases).
## Support
For 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&utm_medium=link&utm_campaign=share-link).
## Development
Development happens on github at
[sourmash-bio/sourmash](https://github.com/sourmash-bio/sourmash).
sourmash is developed in Python and Rust, and you will need a Rust
environment to build it; see [the developer notes](doc/developer.md)
for our suggested development setup.
After installation, `sourmash` is the main command-line entry point;
run it with `python -m sourmash`, or do `pip install -e /path/to/repo` to
do a developer install in a virtual environment.
The `sourmash/` directory contains the Python library and command-line interface code.
The `src/core/` directory contains the Rust library implementing core
functionality.
Tests require py.test and can be run with `make test`.
Please see [the developer notes](doc/developer.md) for more information
on getting set up with a development environment.
CTB
Jan 2024
Raw data
{
"_id": null,
"home_page": null,
"name": "sourmash",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.10",
"maintainer_email": "\"Luiz C. Irber, Jr\" <luiz@sourmash.bio>, \"C. Titus Brown\" <titus@idyll.org>, \"N. Tessa Pierce-Ward\" <ntpierce@ucdavis.edu>",
"keywords": "minhash, bioinformatics",
"author": "Luiz Irber, N. Tessa Pierce-Ward, Mohamed Abuelanin, Harriet Alexander, Abhishek Anant, Keya Barve, Colton Baumler, Olga Botvinnik, Phillip Brooks, Peter Cock, Daniel Dsouza, Jade Gardner, Laurent Gautier, Tim Head, Mahmudur Rahman Hera, Hannah Eve Houts, Lisa K. Johnson, Fabian Kl\u00f6tzl, David Koslicki, Katrin Leinweber, Marisa Lim, Ricky Lim, Bradley Nelson, Ivan Ogasawara, Taylor Reiter, Camille Scott, Andreas Sj\u00f6din, Connor T. Skennerton, Jason Stajich, Daniel Standage, S. Joshua Swamidass, Connor Tiffany, Pranathi Vemuri, Erik Young, Nick H, C. Titus Brown",
"author_email": "Luiz Irber <luiz@sourmash.bio>, N. Tessa Pierce-Ward <tessa@sourmash.bio>",
"download_url": "https://files.pythonhosted.org/packages/45/db/7ca1ce1eedfe86f0094c16809cb5ac444733ea7dc5ad7f3703e4fd607eef/sourmash-4.8.8.tar.gz",
"platform": null,
"description": "# sourmash\n\nQuickly search, compare, and analyze genomic and metagenomic data sets.\n\n[](https://www.repostatus.org/#active)\n<a href=\"https://github.com/sourmash-bio/sourmash/blob/latest/LICENSE\"><img alt=\"License: 3-Clause BSD\" src=\"https://img.shields.io/badge/License-BSD%203--Clause-blue.svg\"></a>\n[](http://sourmash.readthedocs.io/en/latest/)\n[](https://gitter.im/sourmash-bio/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)\n\n[](http://joss.theoj.org/papers/10.21105/joss.00027)\n[](https://github.com/pyOpenSci/software-submission/issues/129)\n\n[](https://anaconda.org/bioconda/sourmash)\n<a href=\"https://pypi.org/project/sourmash/\"><img alt=\"PyPI\" src=\"https://badge.fury.io/py/sourmash.svg\"></a>\n[](https://anaconda.org/conda-forge/sourmash-minimal)\n\n\n\n\n[](https://github.com/sourmash-bio/sourmash/actions/)\n[](https://codecov.io/gh/sourmash-bio/sourmash)\n\n<p align=\"center\"><img src=\"https://raw.githubusercontent.com/sourmash-bio/sourmash/latest/doc/_static/logo.png\" height=\"256\" /></p>\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.00027); please cite that paper if you use sourmash (`doi: 10.21105/joss.00027`):.\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 3.10 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&utm_medium=link&utm_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\n",
"bugtrack_url": null,
"license": "BSD-3-Clause",
"summary": "tools for comparing biological sequences with k-mer sketches",
"version": "4.8.8",
"project_urls": {
"CI": "https://github.com/sourmash-bio/sourmash/actions",
"Documentation": "https://sourmash.readthedocs.io",
"Homepage": "https://sourmash.bio/",
"Source": "https://github.com/sourmash-bio/sourmash",
"Tracker": "https://github.com/sourmash-bio/sourmash/issues"
},
"split_keywords": [
"minhash",
" bioinformatics"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "0147ab15443978de816d423d13595930db8e1c85eaf4c727811cf5528f0c24e5",
"md5": "26cb1f6c0e62147607629e2acf4ebaf4",
"sha256": "6733ffae9299600b57a18ce9c8a06a8da1618bc90506e6c4ad843f6fa3fb6fdf"
},
"downloads": -1,
"filename": "sourmash-4.8.8-py3-none-macosx_10_14_x86_64.whl",
"has_sig": false,
"md5_digest": "26cb1f6c0e62147607629e2acf4ebaf4",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.10",
"size": 2570631,
"upload_time": "2024-04-09T23:04:52",
"upload_time_iso_8601": "2024-04-09T23:04:52.765582Z",
"url": "https://files.pythonhosted.org/packages/01/47/ab15443978de816d423d13595930db8e1c85eaf4c727811cf5528f0c24e5/sourmash-4.8.8-py3-none-macosx_10_14_x86_64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "8b9f3bc03de95d816ba738fe2d3013a7102107895d0982f898343d1f9ddaed7c",
"md5": "a1fcd92679cef41ae848ec969d6463b8",
"sha256": "9b6d76d5706fc0f144e6cc1057941d3bd2779176867feba6e04e7f03d1610b27"
},
"downloads": -1,
"filename": "sourmash-4.8.8-py3-none-macosx_11_0_arm64.whl",
"has_sig": false,
"md5_digest": "a1fcd92679cef41ae848ec969d6463b8",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.10",
"size": 2346642,
"upload_time": "2024-04-09T23:04:57",
"upload_time_iso_8601": "2024-04-09T23:04:57.720395Z",
"url": "https://files.pythonhosted.org/packages/8b/9f/3bc03de95d816ba738fe2d3013a7102107895d0982f898343d1f9ddaed7c/sourmash-4.8.8-py3-none-macosx_11_0_arm64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "1b71e9443277ce1fe40cf632829415385667b97c1a293ee0566c5a021adb6491",
"md5": "df8c791b7e270912e1f6eeb7cb350a3f",
"sha256": "560187f1a34116b9abb4df1536a0c599827af1a942e48cf8cef296a99c6ec628"
},
"downloads": -1,
"filename": "sourmash-4.8.8-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl",
"has_sig": false,
"md5_digest": "df8c791b7e270912e1f6eeb7cb350a3f",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.10",
"size": 2278124,
"upload_time": "2024-04-09T23:05:00",
"upload_time_iso_8601": "2024-04-09T23:05:00.931180Z",
"url": "https://files.pythonhosted.org/packages/1b/71/e9443277ce1fe40cf632829415385667b97c1a293ee0566c5a021adb6491/sourmash-4.8.8-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "e51459e0e24aa2e62a163cb07ebc6da038058846bf7df06f1e6a25d58e2c1354",
"md5": "01a86d42577518f8361f21b697e7ad60",
"sha256": "c0ab053336341cdec0bb42c2bc6326ebbbbaa2ac12d6ad7a0dd49b1d96b81380"
},
"downloads": -1,
"filename": "sourmash-4.8.8-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl",
"has_sig": false,
"md5_digest": "01a86d42577518f8361f21b697e7ad60",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.10",
"size": 4164449,
"upload_time": "2024-04-09T23:05:05",
"upload_time_iso_8601": "2024-04-09T23:05:05.607034Z",
"url": "https://files.pythonhosted.org/packages/e5/14/59e0e24aa2e62a163cb07ebc6da038058846bf7df06f1e6a25d58e2c1354/sourmash-4.8.8-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "edc83461d5ac61e6da92e9a48649c8743ffa413648e5d90d1552b4455b12f82d",
"md5": "875f4ad10eabf348a70ff8e9e79f04bc",
"sha256": "fef5bb197f0f15b04e1d6fd7191630e8e555dfc0e80137a070f6c6b4fed04aa1"
},
"downloads": -1,
"filename": "sourmash-4.8.8-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
"has_sig": false,
"md5_digest": "875f4ad10eabf348a70ff8e9e79f04bc",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.10",
"size": 2802034,
"upload_time": "2024-04-09T23:05:11",
"upload_time_iso_8601": "2024-04-09T23:05:11.076082Z",
"url": "https://files.pythonhosted.org/packages/ed/c8/3461d5ac61e6da92e9a48649c8743ffa413648e5d90d1552b4455b12f82d/sourmash-4.8.8-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "1dd1108db74fbcc8e473a5067c98095a770360e66768489e049f0135a4c06001",
"md5": "accb122662e0abb6a78f716ec6bc97e8",
"sha256": "b366a43e72e2a82fdd3cb11f96413df7b6a06b5d5513e61e605675fc205c409a"
},
"downloads": -1,
"filename": "sourmash-4.8.8-py3-none-win_amd64.whl",
"has_sig": false,
"md5_digest": "accb122662e0abb6a78f716ec6bc97e8",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.10",
"size": 1921922,
"upload_time": "2024-04-09T23:05:13",
"upload_time_iso_8601": "2024-04-09T23:05:13.963018Z",
"url": "https://files.pythonhosted.org/packages/1d/d1/108db74fbcc8e473a5067c98095a770360e66768489e049f0135a4c06001/sourmash-4.8.8-py3-none-win_amd64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "45db7ca1ce1eedfe86f0094c16809cb5ac444733ea7dc5ad7f3703e4fd607eef",
"md5": "ee598d866bf3e5c75dcd3d5682a2339b",
"sha256": "667da4b014f003032bdffa43318bb5668edbbc55055fe109dab959a914d69842"
},
"downloads": -1,
"filename": "sourmash-4.8.8.tar.gz",
"has_sig": false,
"md5_digest": "ee598d866bf3e5c75dcd3d5682a2339b",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.10",
"size": 13280048,
"upload_time": "2024-04-09T23:09:22",
"upload_time_iso_8601": "2024-04-09T23:09:22.368105Z",
"url": "https://files.pythonhosted.org/packages/45/db/7ca1ce1eedfe86f0094c16809cb5ac444733ea7dc5ad7f3703e4fd607eef/sourmash-4.8.8.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-04-09 23:09:22",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "sourmash-bio",
"github_project": "sourmash",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [],
"tox": true,
"lcname": "sourmash"
}
