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ACCUSA: accurate SNP calling on draft genomes

Item Type:Article
Title:ACCUSA: accurate SNP calling on draft genomes
Creators Name:Froehler, S. and Dieterich, C.
Abstract: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 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'), which 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 current SNP calling software in detecting true SNPs. More important, 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: Sebastian.Froehler@mdc-berlin.de and Christoph.Dieterich@mdc-berlin.de.
Keywords:Genome, Genomics, Single Nucleotide Polymorphism, Saccharomyces cerevisiae, Software
Publisher:Oxford University Press
Page Range:1364-1365
Date:15 May 2010
Official Publication:https://doi.org/10.1093/bioinformatics/btq138
PubMed:View item in PubMed

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