Quake: quality-aware detection and correction of sequencing errors

Genome Biol. 2010;11(11):R116. doi: 10.1186/gb-2010-11-11-r116. Epub 2010 Nov 29.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • DNA, Bacterial / genetics
  • Escherichia coli / genetics
  • Genome, Human
  • Humans
  • Likelihood Functions
  • Models, Biological
  • Polymorphism, Single Nucleotide
  • Sequence Alignment*
  • Sequence Analysis, DNA / methods*
  • Software*


  • DNA, Bacterial