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

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

Research output: Contribution to journalArticleAcademicpeer-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 languageEnglish
Number of pages13
JournalPLOS one
Publication statusPublished - 1 Apr 2015

Keywords

  • bioinformatics

Cite this

Warris, Sven ; Yalcin, Feyruz ; Jackson, Katherine J.L. ; Nap, Jan Peter. / Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS. In: PLOS one. 2015.
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Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS. / Warris, Sven; Yalcin, Feyruz; Jackson, Katherine J.L. ; Nap, Jan Peter.

In: PLOS one, 01.04.2015.

Research output: Contribution to journalArticleAcademicpeer-review

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AB - 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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