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Publication Detail
Which is faster: Bowtie2GP $>$ Bowtie $>$ Bowtie2 $>$ BWA
  • Publication Type:
    Report
  • Authors:
    Langdon WB
  • publication date:
    21/01/2013
  • Place of publication:
    Department of Computer Science, University College London
  • Report number:
    RN/13/03
  • Notes:
    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. size: 4 pages notes: GISMOE. Available as http://arxiv.org/abs/1301.5187 and GECCO 2013 late breaking abstract \citeLangdon:2013:GECCOlb. See also \citeLangdon:RN1209. Bowtie2GP and test dataset available via http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/gp-code/bowtie2gp
Abstract
We have recently used genetic programming to automatically generate an improved version of Langmead’s DNA read alignment tool Bowtie2 Sect.5.3 \citeLangdon: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 genome.
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