SSW

Description

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. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our 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.

More information

• Homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library

Availability

Module	NIC5	Hercules2	Dragon2	Lemaitre3	Dragon1
SSW/1.1-GCCcore-10.2.0		✓
SSW/1.1-GCCcore-11.2.0	✓	✓