Introduction

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.

Publications

  1. ACCUSA--accurate SNP calling on draft genomes.
    Cite this
    Fröhler S, Dieterich C, 2010-05-01 - Bioinformatics (Oxford, England)
  2. ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores.
    Cite this
    Piechotta M, Dieterich C, 2013-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Sebastian Fröhler
    Developer

  2. Christoph Dieterich
    Investigator

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Summary
AccessionBT006461
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByChristoph Dieterich