Python bindings for Complete-Striped-Smith-Waterman-Library (SSW) project
Project description
# 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](https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library)
Please cite this [PLOS ONE paper](http://dx.plos.org/10.1371/journal.pone.0082138) 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](https://genome.sph.umich.edu/wiki/SAM#What_is_a_CIGAR.3F)) 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](https://pypi.org/project/ssw-py/)
$ pip install ssw-py
or from source
$ python setup.py install
## Documentation See [documentation](https://libnano.github.io/ssw-py/) for help on using these bindings.
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