Abstract
BackgroundBarraCUDA 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”.ResultsThe 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.ConclusionsThe speed up was such that the GI version was adopted and has been regularly downloaded from SourceForge for more than 12 months.
Highlights
NextGen DNA sequence alignment Both version of BarraCUDA and bwa use the Burrows-Wheeler algorithm
Why run bioinformatics on gaming machines Bioinformaticians have seized the advantages of using computer graphics hardware (GPUs) [1], those made by nVidia
[3] we presented an approach in which a small part of the manually written code had been optimised by a variant of genetic programming [4, 5] to give a huge speed up on that part. (The raw graphics kernel can process well over a million DNA sequences a second ([3], Fig. 1))
Summary
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
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