SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications.

ABSTRACT:

Background

The Smith-Waterman 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 for next-generation sequencing data. Though various fast Smith-Waterman implementations are developed, they are either designed as monolithic protein database searching tools, which do not return detailed alignment, or are embedded into other tools. These issues make reusing these efficient Smith-Waterman implementations impractical.

Results

To facilitate easy integration of the fast Single-Instruction-Multiple-Data Smith-Waterman algorithm into third-party software, we wrote a C/C++ library, which extends Farrar's Striped Smith-Waterman (SSW) to return alignment inform

SUBMITTER: Zhao M 

PROVIDER: S-EPMC3852983 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature