A tandem simulation framework for predicting mapping quality

Ben Langmead

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Read alignment is the first step in most sequencing data analyses. Because a read's point of origin can be ambiguous, aligners report a mapping quality, which is the probability that the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality. I describe a framework for predicting mapping qualities that works by simulating a set of tandem reads. These are like the input reads in important ways, but the true point of origin is known. I implement this method in an accurate and low-overhead tool called Qtip, which is compatible with popular aligners.

Original languageEnglish (US)
Article number152
JournalGenome biology
Issue number1
StatePublished - Aug 10 2017


  • Mapping
  • Quality
  • Read alignment
  • Sequencing

ASJC Scopus subject areas

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


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