- author = "W. B. Langdon",
- title = "Which is faster: {Bowtie2GP} $>$ {Bowtie} $>$ {Bowtie2} $>$ {BWA}",
- institution = "Department of Computer Science, University College London",
- year = "2013",
- type = "Research Note",
- number = "RN/13/03",
- address = "Gower Street, London WC1E 6BT, UK",
- month = "21 " # jan,
- keywords = "genetic algorithms, genetic programming, genetic improvement, 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 genome.",
-
notes = "GISMOE. Available as http://arxiv.org/abs/1301.5187
and GECCO 2013 late breaking abstract
\cite{Langdon:2013:GECCOlb}.
See also \cite{Langdon:2013:ieeeTEC} \cite{Langdon:RN1209}.
Bowtie2GP and test dataset available via http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/gp-code/bowtie2gp",
