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arXiv · 1505.07855

Genetically Improved BarraCUDA

W. B. Langdon·Brian Yee Hong Lam
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Abstract

BarraCUDA is a C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. The genetically improved (GI) code is up to three times faster on short paired end reads from The 1000 Genomes Project and 60percent 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 CPU.

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W. B. Langdon, Brian Yee Hong Lam. 2015-05-28. Genetically Improved BarraCUDA. https://doi.org/10.1186/s13040-017-0149-1

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