Compute and compare MinHash signatures for DNA data sets.
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README.md

sourmash

Documentation Build Status codecov DOI

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

Sourmash is published on JOSS.


The name is a riff off of Mash, combined with @ctb's love of whiskey. (Sour mash is used in making whiskey.)

Authors: C. Titus Brown (@ctb) and Luiz C. Irber, Jr (@luizirber).

sourmash is a product of the Lab for Data-Intensive Biology at the UC Davis School of Veterinary Medicine.

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 ijson, 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. The developers sometimes hang out on gitter.

Development

Development happens on github at 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