Which is faster: Bowtie2GP $>$ Bowtie $>$ Bowtie2 $>$ BWA

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

  author =       "W. B. Langdon",
  title =        "Which is faster: {Bowtie2GP} $>$ {Bowtie} $>$
                 {Bowtie2} $>$ {BWA}",
  institution =  "Department of Computer Science, University College
  year =         "2013",
  type =         "Research Note",
  number =       "RN/13/03",
  address =      "Gower Street, London WC1E 6BT, UK",
  month =        "21 " # jan,
  keywords =     "genetic algorithms, genetic programming, automatic
                 software re-engineering, SBSE, double-ended DNA
                 sequence, Solexa nextgen NGS, sequence query,
                 Smith-Waterman, Bowtie2GP, fuzzy string matching, Homo
                 sapiens genome reference consortium GRCh37.p5
                 h_sapiens_37.5_asm, IP29.",
  URL =          "http://www.cs.ucl.ac.uk/fileadmin/UCL-CS/research/RN_13_03.pdf",
  URL =          "http://arxiv.org/abs/1301.5187",
  size =         "4 pages",
  abstract =     "We have recently used genetic programming to
                 automatically generate an improved version of
                 Langmead's DNA read alignment tool Bowtie2 Sect.5.3
                 \cite{Langdon:RN1209}. We find it runs more than four
                 times faster than the Bioinformatics sequencing tool
                 (BWA) currently used with short next generation paired
                 end DNA sequences by the Cancer Institute, takes less
                 memory and yet finds similar matches in the human
  notes =        "GISMOE. Available as http://arxiv.org/abs/1301.5187
                 and GECCO 2013 late breaking abstract

                 See also \cite{Langdon:2013:ieeeTEC}

                 Bowtie2GP and test dataset available via

Genetic Programming entries for William B Langdon