Ssw

#SSW: A Python Wrapper for the SIMD Smith-Waterman

Overview

SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the CPU level. This repository wraps the SSW library into an easy to install, high-level python interface with no external library dependancies.

The SSW library is written by Mengyao Zhao and Wan-Ping Lee, and this python interface is maintained by Giles Hall.

Installation

To install the SSW python package, use pip:

$ pip install ssw

Example Usage

import ssw
aligner = ssw.Aligner()
alignment = aligner.align(reference="ACGTGAGAATTATGGCGCTGTGATT", query="ACGTGAGAATTATGCGCTGTGATT")
print(alignment.alignment_report())
Score = 45, Matches = 24, Mismatches = 0, Insertions = 0, Deletions = 1

ref   1   ACGTGAGAATTATGGCGCTGTGATT
          ||||||||||||| |||||||||||
query 1   ACGTGAGAATTAT-GCGCTGTGATT