14064

Genetically Improved BarraCUDA

W. B. Langdon, Brian Yee Hong Lam
UCL Department of Computer Science
arXiv:1505.07855 [q-bio.GN], (28 May 2015)

@article{langdon2015genetically,

   title={Genetically Improved BarraCUDA},

   author={Langdon, W. B. and Lam, Brian Yee Hong},

   year={2015},

   month={may},

   archivePrefix={"arXiv"},

   primaryClass={q-bio.GN}

}

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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 60 percent 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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