PT - JOURNAL ARTICLE AU - Ben Langmead TI - A tandem simulation framework for predicting mapping quality AID - 10.1101/103952 DP - 2017 Jan 01 TA - bioRxiv PG - 103952 4099 - http://biorxiv.org/content/early/2017/05/04/103952.short 4100 - http://biorxiv.org/content/early/2017/05/04/103952.full AB - 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: the probability the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality. We describe a framework for predicting mapping qualities that works by simulating a set of tandem reads, similar to the input reads in important ways, but for which the true point of origin is known. We implement this in an accurate and low-overhead tool called Qtip, which is compatible with popular aligners.