Compute MinHash signatures for DNA sequences.
sourmash compute *.fq.gz sourmash compare *.sig -o distances sourmash plot distances
We have demo notebooks on binder that you can interact with:
Sourmash is published on JOSS.
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
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