Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS

Sven Warris; Feyruz Yalcin; Katherine J.L.  Jackson; Jan Peter Nap

Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS

Sven Warris, Feyruz Yalcin, Katherine J.L. Jackson, Jan Peter Nap

Life Sciences & Renewable Energy

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis.

Original language	English
Number of pages	13
Journal	PLoS ONE
Publication status	Published - 1 Apr 2015

Keywords

bioinformatics

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abstract = "To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis.",

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