Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks.

ABSTRACT:

Background

Genetic studies are increasingly based on short noisy next generation scanners. Typically complete DNA sequences are assembled by matching short NextGen sequences against reference genomes. Despite considerable algorithmic gains since the turn of the millennium, matching both single ended and paired end strings to a reference remains computationally demanding. Further tailoring Bioinformatics tools to each new task or scanner remains highly skilled and labour intensive. With this in mind, we recently demonstrated a genetic programming based automated technique which generated a version of the state-of-the-art alignment tool Bowtie2 which was considerably faster on short sequences produced by a scanner at the Broad Institute and released as part of The Thousand Genome Pro

SUBMITTER: Langdon WB 

PROVIDER: S-EPMC4304608 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature