Skip to main content

tools for comparing DNA sequences with MinHash sketches

Project description

# sourmash

[![Documentation](https://readthedocs.org/projects/sourmash/badge/?version=latest)](http://sourmash.readthedocs.io/en/latest/)
[![Build Status](https://drone.io/github.com/dib-lab/sourmash/status.png)](https://drone.io/github.com/dib-lab/sourmash/latest)
[![codecov](https://codecov.io/gh/dib-lab/sourmash/branch/master/graph/badge.svg)](https://codecov.io/gh/dib-lab/sourmash)
[![DOI](https://zenodo.org/badge/22555/dib-lab/sourmash.svg)](https://zenodo.org/badge/latestdoi/22555/dib-lab/sourmash)

Compute MinHash signatures for DNA sequences.

Usage:

sourmash compute *.fq.gz
sourmash compare *.sig -o distances
sourmash plot distances

We have demo notebooks on binder that you can interact with:

[![Binder](http://mybinder.org/badge.svg)](http://mybinder.org/repo/dib-lab/sourmash)

----

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.)

Authors: [C. Titus Brown](mailto:titus@idyll.org) ([@ctb](http://github.com/ctb)) and Luiz C. Irber, Jr.

sourmash is a product of the
[Lab for Data-Intensive Biology](http://ivory.idyll.org/lab/) at the
[UC Davis School of Veterinary Medicine](http://www.vetmed.ucdavis.edu).

## Installation

You can do:

pip install sourmash

sourmash runs under both Python 2.7.x and Python 3.5. The base
requirements are screed and PyYAML, together with a C++ development
environment and the CPython development headers and libraries (for the
C++ extension).

The comparison code (`sourmash compare`) uses numpy, and the plotting
code uses matplotlib and scipy, but most of the code is usable without
these.

## Support

Please ask questions and files issues
[on Github](https://github.com/dib-lab/sourmash/issues). The developers
sometimes hang out [on gitter](https://gitter.im/dib-lab/khmer).

## Development

Development happens on github at
[dib-lab/sourmash](https://github.com/dib-lab/sourmash).

`sourmash` is the main command-line entry point; run it for help.

`sourmash_lib/` contains the library code.

Tests require py.test and can be run with `make test`.

----

CTB

6.jun.2016

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for sourmash, version 0.9.5
Filename, size File type Python version Upload date Hashes
Filename, size sourmash-0.9.5-cp27-cp27m-macosx_10_11_intel.whl (50.2 kB) File type Wheel Python version 2.7 Upload date Hashes View hashes
Filename, size sourmash-0.9.5.tar.gz (34.4 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page