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Genetically improved BarraCUDA
W B Langdon1, Brian Yee Hong Lam2
1Department of Computer Science, University College London, Gower Street, London, WC1E 6BT UK.
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.
