Genetically Improved BarraCUDA

Created by W.Langdon from gp-bibliography.bib Revision:1.3872

@Article{Langdon:2017:BDM,
  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.

                 Results:

                 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.

                 Conclusions:

                 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

Citations