Quake: quality-aware detection and correction of sequencing errors.
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.
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, and Department of Computer Science, University of Maryland, College Park, MD 20742, USA. dakelley@umiacs.umd.edu
David R
DR
Kelley
Michael C
MC
Schatz
Steven L
SL
Salzberg
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D016013:Likelihood Functions; D008954:Models, Biological; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D004269:DNA, Bacterial