Supplementary Figure 1: Alignment speed and sensitivity of spliced alignment software for 40 million error-free simulated paired-end reads (100 bp long, 20 million pairs).
From: HISAT: a fast spliced aligner with low memory requirements
This figure shows the alignment speed and sensitivity for each type of pair (all, M, 2M_gt_15, 2M_8_15, 2M_1_7, gt_2M, where ‘all’ includes all the pair types). Since a pair consists of left and right reads, the type of a pair is determined by the more difficult read type. The difficulties of read types are given in the following order from easiest to most difficult: M, 2M_gt_15, 2M_8_15, 2M_1_7, and gt_2M. The plot on the left shows the alignment speed of the programs in terms of the number of pairs processed per second. The right plot shows alignment sensitivity. Pairs are categorized as: (1) correctly and uniquely mapped, (2) correctly mapped (multi-mapped), (3) incorrectly mapped, and (4) unmapped. Case (2) covers instances where an aligner mapped a pair to multiple locations and one of the locations was correct. These four categories encompass all of the pairs. The numbers in the right plot represent the percentages of case (1). The numbers inside the parentheses represent the percentages of cases (1) and (2) combined.
