ACCUSA--accurate SNP calling on draft genomes

Bioinformatics. 2010 May 15;26(10):1364-5. doi: 10.1093/bioinformatics/btq138. Epub 2010 Apr 1.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genome*
  • Genomics / methods*
  • Polymorphism, Single Nucleotide*
  • Saccharomyces cerevisiae / genetics
  • Software*