Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome.BACKGROUND
 The use of artificial data to evaluate the performance of aligners and peak callers not only improves its accuracy and reliability, but also makes it possible to reduce the computational time.  In this paper, we compared the accuracy of the performance of seven aligners on well-controlled simulated benchmark data which was sampled from a single chromosome and also from a whole genome.  We found that commonly used statistical methods are insufficient to evaluate an aligner performance, and applied a novel measure of a read density distribution similarity, which allowed to reveal artefacts in aligners' performances.  The proposed quality assessment method allows to identify the inherent shortcoming of aligners that are not detected by conventional statistical methods, and can affect the quality of alignment of real data.
aligner
The use of artificial data to evaluate the performance of aligners and peak callers not only improves its accuracy and reliability, but also makes it possible to reduce the computational time. 
peak caller