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Quake: quality-aware detection and correction of sequencing errors

David R Kelley1*, Michael C Schatz2 and Steven L Salzberg1

Author Affiliations

1 Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, and Department of Computer Science, University of Maryland, College Park, MD 20742, USA

2 Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA

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Genome Biology 2010, 11:R116  doi:10.1186/gb-2010-11-11-r116

Published: 29 November 2010

Abstract

We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accuracy on realistically simulated reads. We further demonstrate substantial improvements in de novo assembly and SNP detection after using Quake. Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake webcite.