tools for comparing DNA sequences with MinHash sketches
Project description
# sourmash
[](http://sourmash.readthedocs.io/en/latest/)
[](https://drone.io/github.com/dib-lab/sourmash/latest)
[](https://codecov.io/gh/dib-lab/sourmash)
[](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:
[](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
[](http://sourmash.readthedocs.io/en/latest/)
[](https://drone.io/github.com/dib-lab/sourmash/latest)
[](https://codecov.io/gh/dib-lab/sourmash)
[](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:
[](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
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