SSW

SSW implements the Striped Smith-Waterman algorithm to compute optimal pairwise local alignments between two sequences for genomic analyses and next-generation sequencing applications.

Key Features:

• Optimal Pairwise Alignment: Generates precise optimal Smith-Waterman alignments and detailed alignment information for accurate read mapping and variation detection.
• Fast Performance: Utilizes a Single-Instruction-Multiple-Data (SIMD) striped implementation to accelerate Smith-Waterman computations.
• Flexible API: Provided as a C/C++ library for integration into third-party bioinformatics software.
• Full alignment and suboptimal scores: Produces full optimal alignment results and reports suboptimal alignment scores.
• Linear-space complexity: Incorporates methods to compute alignments with linear space complexity to reduce memory usage.

Scientific Applications:

• Tool integration: Employed as the primary read mapper in MOSAIK, to enhance split-read mapping in SCISSORS, to aid mobile element insertion (MEI) detection in TANGRAM, and to support read-overlap graph generation in RZMBLR.
• Acceleration of existing modules: Used to replace standard or banded Smith-Waterman modules in pipelines to achieve significant speed improvements.

Methodology:

Extends Farrar's Striped Smith-Waterman algorithm using a SIMD striped approach and implements linear-space methods to produce full optimal alignments alongside suboptimal scores.