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.
[1]
Gonçalo R. Abecasis,et al.
The Sequence Alignment/Map format and SAMtools
,
2009,
Bioinform..
[2]
Juliane C. Dohm,et al.
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
,
2008,
Nucleic acids research.
[3]
Gabor T. Marth,et al.
A general approach to single-nucleotide polymorphism discovery
,
1999,
Nature Genetics.
[4]
Leopold Parts,et al.
Population genomics of domestic and wild yeasts
,
2008
.
[5]
Robert P. Davey,et al.
Population genomics of domestic and wild yeasts
,
2008,
Nature.
[6]
M. Metzker.
Sequencing technologies — the next generation
,
2010,
Nature Reviews Genetics.