Quake: Quality-aware detection and correction of sequencing errors

David R. Kelley, Michael C. Schatz, Steven L Salzberg

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article numberR116
JournalGenome Biology
Volume11
Issue number11
DOIs
StatePublished - Nov 29 2010
Externally publishedYes

Fingerprint

Software
sequence analysis
nucleotides
software
DNA Sequence Analysis
Single Nucleotide Polymorphism
Nucleotides
DNA
detection
project
programme
rate

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Quake : Quality-aware detection and correction of sequencing errors. / Kelley, David R.; Schatz, Michael C.; Salzberg, Steven L.

In: Genome Biology, Vol. 11, No. 11, R116, 29.11.2010.

Research output: Contribution to journalArticle

Kelley, David R. ; Schatz, Michael C. ; Salzberg, Steven L. / Quake : Quality-aware detection and correction of sequencing errors. In: Genome Biology. 2010 ; Vol. 11, No. 11.
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