A new paper describing a tandem simulation framework for predicting mapping quality was published in Genome Biology.  The paper describes the free, open source Qtip software.

Mapping qualities are important quantities in the world of next-gen sequencing analysis. A mapping quality quantifies the read aligner’s confidence that the reported alignment for a sequencing read is the correct one. Without accurate mapping qualities, downstream tools like variant callers cannot judge which alignments are reliable, and results suffer. There is copious literature on making alignment algorithms more efficient, but very little on the topic of making better mapping-quality predictions.

This paper describes a new “tandem simulation” 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. The method is implemented in an accurate and low-overhead tool called Qtip, compatible with the popular aligners Bowtie 2, BWA-MEM and SNAP.