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Publication Detail
Genetically Improved BarraCUDA
  • Publication Type:
    Report
  • Authors:
    Langdon WB, Lam BYH
  • publication date:
    28/05/2015
  • Place of publication:
    Department of Computer Science, University College London
  • Report number:
    RN/15/03
  • Addresses:
    Gower Street, London WC1E 6BT, UK
  • Notes:
    keywords: GPGPU, parallel computing, genetic improvement, double-ended DNA sequence, nextgen NGS, sequence query, Homo sapiens genome reference consortium size: 8 pages notes: Benchmarks \citeLangdon:2015:GECCO almost no mention of GP.
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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