SSW 1.1-GCCcore-11.3.0

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.

Accessing SSW 1.1-GCCcore-11.3.0

To load the module for SSW 1.1-GCCcore-11.3.0 please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load bear-apps/2022a
module load SSW/1.1-GCCcore-11.3.0

BEAR Apps Version

2022a

Architectures

EL8-cascadelake — EL8-icelake — EL8-sapphirerapids

The listed architectures consist of two part: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

More Information

For more information visit the SSW website.

Dependencies

This version of SSW has a direct dependency on: GCCcore/11.3.0 zlib/1.2.12-GCCcore-11.3.0

Required By

This version of SSW is a direct dependent of: SeqLib/1.2.0-GCC-11.3.0

Last modified on 3rd November 2023