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.
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.
if you would like to learn more about this application and our high-performance reconfigurable hardware.