Genetically Improved BarraCUDA

Created by W.Langdon from gp-bibliography.bib Revision:1.4020

  author =       "W. B. Langdon and Brian Yee Hong Lam",
  title =        "Genetically Improved {BarraCUDA}",
  journal =      "BioData Mining",
  year =         "2017",
  volume =       "20",
  number =       "28",
  month =        "2 " # aug,
  keywords =     "genetic algorithms, genetic programming, genetic
                 improvement, GPGPU, parallel computing, double-ended
                 DNA sequence, nextgen NGS",
  DOI =          "doi:10.1186/s13040-017-0149-1",
  size =         "11 pages",
  abstract =     "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.


                 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
        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.


                 The speed up was such that the GI version was adopted
                 and has been regularly downloaded from SourceForge for
                 more than 12 months.",
  notes =        "Replaces RN/15/03 \cite{Langdon:RN1503}

                 PMID: 28785314",

Genetic Programming entries for William B Langdon Brian Yee Hong Lam