Fig. 3

SyRI’s performance compared to six other tools on simulated assemblies. a Ratio of rearrangements accurately predicted by each of the tools. b Sensitivity (green points) and precision (orange points) values for the prediction of indels. For indels, we compared the location and size of the predicted indels with the simulated indels, allowing for error in both location and size. Two different error limits were used: 5 and 100 bp. Values are averages from the analysis of 100 simulated genomes. “Not Applicable” implies that the specific tool is not designed to identify the specific genomic difference. Background colors represent the data type required by the respective tools (from white to dark gray: chromosome-level de novo assembly, de novo assembly, long sequencing reads (both PacBio (PB) and Oxford Nanopore (ONT) reads), short sequencing reads)