[Debian-med-packaging] Bug#828042: ITP: libssw -- fast SIMD parallelized implementation of the Smith-Waterman algorithm

[Sascha Steinbiss]

Package: wnpp
Severity: wishlist
Owner: Sascha Steinbiss <satta at debian.org>

* Package name    : libssw
  Version         : git20160511.7d84de2
  Upstream Author : Mengyao Zhao <zhaomengyao at gmail.com>
* URL             : https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
* License         : MIT
  Programming Lang: C
  Description     : fast SIMD parallelized implementation of the Smith-Waterman algorithm

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 instruction level. The SSW library provides an API that can be
flexibly used by programs written in C, C++ and other languages. The library
can do protein and genome alignment directly.
The current version of this implementation is ~50 times faster than an ordinary
Smith-Waterman. It can return 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.

This package will be maintained by the Debian Med Packaging Team as a
dependency for SPAdes, to replace code currently embedded there.