Fig. 3From: A tandem simulation framework for predicting mapping qualityStages of the Qtip pipeline. Computational steps and intermediate results in Qtip. Numbers denote ordering of steps and arrows denote the flow of data. The input (upper left) is a collection of sequencing reads and the ultimate output (upper right) is a SAM file containing alignments, where each aligned read’s MAPQ field is set according to Qtip’s predictionBack to article page