W B. Langdon
ABSTRACT
We have recently used genetic programming to automatically generate an improved version of Langmead's DNA read alignment tool Bowtie2 [RN/12/09, Sect.5.3]. 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.
- William B. Langdon and Mark Harman, "Genetically improving 50000 lines of C++," Research Note RN/12/09, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK, 19 Sept. 2012.Google Scholar
- Ben Langmead and Steven L Salzberg, "Fast gapped-read alignment with Bowtie 2," Nature Methods, vol. 9, no. 4, pp. 357--359, 4 March 2012.Google ScholarCross Ref
- Riccardo Poli, William B. Langdon, and Nicholas Freitag McPhee, A field guide to genetic programming, Published via http://lulu.com and freely available at http://www.gp-field-guide.org.uk, 2008, (With contributions by J. R. Koza). Google ScholarDigital Library
- Heng Li and Richard Durbin, "Fast and accurate long-read alignment with Burrows-Wheeler transform," Bioinformatics, vol. 26, no. 5, pp. 589--595, 2010. Google ScholarDigital Library
- Nuno A. Fonseca, Johan Rung, Alvis Brazma, and John C. Marioni, "Tools for mapping high-throughput sequencing data," Bioinformatics, vol. 28, no. 24, pp. 3169--3177, 2012. Google ScholarDigital Library
- Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman, "Gapped BLAST and PSI-BLAST a new generation of protein database search programs," Nucleic Acids Research, vol. 25, no. 17, pp. 3389--3402, 1997.Google ScholarCross Ref
- Which is faster: bowtie2GP bowtie > bowtie2 > BWA
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