Which is faster: bowtie2GP bowtie bowtie2 BWA

Authors:
W B. Langdon
Affiliations:
University College London, London, APO AA
Venue:
Proceedings of the 15th annual conference companion on Genetic and evolutionary computation
Year:
2013

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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.