SSW Library

swMATH ID: 33167
Software Authors: Mengyao Zhao, Wan-Ping Lee, Erik Garrison, Gabor T. Marth
Description: SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications. The Smith Waterman (SW) algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools, but current implementations are either designed as monolithic protein database searching tools or are embedded into other tools. To facilitate easy integration of the fast Single Instruction Multiple Data (SIMD) SW algorithm into third party software, we wrote a C/C++ library, which extends Farrars Striped SW (SSW) to return alignment information in addition to the optimal SW score. Availability: SSW is available both as a C/C++ software library, as well as a stand alone alignment tool wrapping the librarys functionality at this https URL Striped-Smith-Waterman-Library Contact: marth@bc.edu
Homepage: https://arxiv.org/abs/1208.6350
Keywords: Genomics; arXiv_q-bio.GN; Smith Waterman (SW); Genomic Applications; C/C++ Library; Farrars Striped SW
Related Software: GeneOptimizer; MUSCLE
Cited in: 0 Publications