RT Journal Article
SR Electronic
T1 Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 007641
DO 10.1101/007641
A1 Richard Wilton
A1 Tamas Budavari
A1 Ben Langmead
A1 Sarah Wheelan
A1 Steven L. Salzberg
A1 Alex Szalay
YR 2014
UL http://biorxiv.org/content/early/2014/08/01/007641.abstract
AB Motivation In computing pairwise alignments of biological sequences, software implementations employ a variety of heuristics that decrease the computational effort involved in computing potential alignments. A key element in achieving high processing throughput is to identify and prioritize potential alignments where high-scoring mappings can be expected. These tasks involve listprocessing operations that can be efficiently performed on GPU hardware.Results We implemented a read aligner called A21 that exploits GPU-based parallel sort and reduction techniques to restrict the number of locations where potential alignments may be found. When compared with other high-throughput aligners, this approach finds more high-scoring mappings without sacrificing speed or accuracy. A21 running on a single GPU is about 10 times faster than comparable CPU-based tools; it is also faster and more sensitive in comparison with other recent GPU-based aligners.Availability The A21 software is open source and available at https://github.com/RWilton/A21.Contact rwilton{at}pha.jhu.eduSupplementary information Supplementary results are available at <<<TBD>>>