title: ACCUSA--accurate SNP calling on draft genomes.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  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.
  
  
  BACKGROUND
  christoph.dieterich@mdc-berlin.de
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Bioinformatics in Quantitative Biology, The Berlin Institute for Medical Systems Biology at Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin-Buch, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Fröhler
authors.forename: Christoph
authors.initials: C
authors.lastname: Dieterich
mesh_terms: D016678:Genome; D023281:Genomics / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software