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| 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 |
| Source: | Bioinformatics |
| ISSN: | 1367-4803 |
| Publisher: | Oxford University Press |
| Volume: | 26 |
| Number: | 10 |
| 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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