SSW

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.

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

Available modules

The overview below shows which SSW installations are available per target architecture in the HPCC module system, ordered based on software version (new to old).

To start using SSW, load one of these modules using a module load command like:

module load SSW/1.1-GCCcore-12.3.0

(This data was automatically generated on Thu, 10 Jul 2025 at 12:00:14 EDT)

	gateway	generic	zen2	zen3	zen4	haswell	skylake_avx512
	Gateway nodes	everywhere (except Grace nodes)	amd20	amd22	amd24	intel16	intel18,amd20-v100,amd21,intel21
SSW/1.1-GCCcore-12.3.0	-	x	-	-	-	-	-