ssw-py: Striped Smith-Waterman SIMD accelerated Python Package for Use in Genomic Applications

This library uses the excellent source code from this is original source repository

Please cite this PLOS ONE paper by Zhao et al. 2013 when using this software.

Overview

ssw-py provides a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level.

Using ssw.AlignmentMgr, you can compute the Smith-Waterman score, alignment location and traceback path (CIGAR) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.

Note: When Striped Smith-Waterman opens a gap, the gap open penalty alone is applied.

Installation

from PyPi

$ pip install ssw-py

or from source

$ python setup.py install

Documentation

See documentation for help on using these bindings.