Journal Article

ACCUSA—accurate SNP calling on draft genomes

Sebastian Fröhler and Christoph Dieterich

in Bioinformatics

Volume 26, issue 10, pages 1364-1365
Published in print May 2010 | ISSN: 1367-4803
Published online April 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq138
ACCUSA—accurate SNP calling on draft genomes

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Summary: Next generation sequencing technologies facilitate genome-wide analysis of several biological processes. We are interested in whole-genome genotyping. To our knowledge, none of the existing single nucleotide polymorphism (SNP) callers consider the quality of the reference genome, which is not necessary for high-quality assemblies of well-studied model organisms. However, most genome projects will remain in draft status with little to no genome assembly improvement due to time and financial constraints. Here, we present a simple yet elegant solution (‘ACCUSA’) that considers both the read qualities as well as the reference genome's quality using a Bayesian framework. We demonstrate that ACCUSA is as good as the current SNP calling software in detecting true SNPs. More importantly, ACCUSA does not call spurious SNPs, which originate from a poor reference sequence.

Availability: ACCUSA is available free of charge to academic users and may be obtained from ftp://bbc.mdc-berlin.de/software. ACCUSA is programmed in JAVA 6 and runs on any platform with JAVA support.

Contact: christoph.dieterich@mdc-berlin.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1084 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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