Python bindings for Complete-Striped-Smith-Waterman-Library (SSW) project

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

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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.

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