SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

TL;DR

The paper introduces SSW, a C/C++ library implementing SIMD-accelerated Smith-Waterman algorithm, designed for easy integration into genomic tools, providing optimal alignment scores and detailed alignment information.

Contribution

It presents a new SIMD-based Smith-Waterman library that extends existing methods to include alignment details, facilitating integration into genomic applications.

Findings

Efficient SIMD implementation of Smith-Waterman.

Provides alignment details alongside scores.

Easy to integrate into third-party software.

Abstract

Summary: 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 https://github.com/mengyao/Complete- Striped-Smith-Waterman-Library Contact: marth@bc.edu