Home Company News & Events New accelerated Smith-Waterman available
New accelerated Smith-Waterman available

April 4th, 2012 - SciEngines is happy to announce the availability of a new accelerated version of the Smith-Waterman algorithm for high-quality alignment of genetic sequences.

This new version of Smith-Waterman is featuring a variety of settings and is further improved in speed. 3 TCUPS on a RIVYERA S3-5000 when analysing real-live NGS human genome data is reached.

Features include:

User-definable scoring matrix, affine gap penalties support, calculation of reverse complement, multiple query files as well as multiple database files for accelerated sequence alignment.

Currently, plain-Text output as well as SAM output is supported and a command-line interface with commands equal to NCBI versions allows integration into analysis pipelines. An integration with the workbenches from CLC bio is underway.

 

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