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ACCUSA - Accurate SNP calling on draft genomes manuscript accepted

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.

This manuscript by Fröhler and Dieterich will appear in OUP Bioinformatics. ( online access )

 

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