Genetically improved BarraCUDA.
Published version
Peer-reviewed
Repository URI
Repository DOI
Change log
Authors
Langdon, WB
Lam, Brian Yee Hong
Abstract
BACKGROUND: BarraCUDA is an open source C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. Recently its source code was optimised using "Genetic Improvement". RESULTS: The genetically improved (GI) code is up to three times faster on short paired end reads from The 1000 Genomes Project and 60% more accurate on a short BioPlanet.com GCAT alignment benchmark. GPGPU BarraCUDA running on a single K80 Tesla GPU can align short paired end nextGen sequences up to ten times faster than bwa on a 12 core server. CONCLUSIONS: The speed up was such that the GI version was adopted and has been regularly downloaded from SourceForge for more than 12 months.
Description
Keywords
Double-ended DNA sequence, GPGPU, Genetic improvement, Nextgen NGS, Parallel computing
Journal Title
BioData Min
Conference Name
Journal ISSN
1756-0381
1756-0381
1756-0381
Volume Title
10
Publisher
Springer Science and Business Media LLC