Quake: Quality-aware detection and correction of sequencing errors

Kelley, D. R., Schatz, M. C., Salzberg, S. L. (November 2010) Quake: Quality-aware detection and correction of sequencing errors. Genome Biology, 11 (11). ISSN 1474-7596

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URL: http://www.ncbi.nlm.nih.gov/pubmed/21114842
DOI: 10.1186/gb-2010-11-11-r116

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. © 2010 Kelley et al.; licensee BioMed Central Ltd.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism
CSHL Authors:
Communities: CSHL labs > Schatz lab
CSHL Cancer Center Program > Cancer Genetics
Depositing User: CSHL Librarian
Date: 29 November 2010
Date Deposited: 04 Oct 2011 14:19
Last Modified: 14 Oct 2015 18:37
PMCID: PMC3156955
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15450

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