Fig. 6

Benchmarks of recall/error rate and dependence of precision on reference genome, for pandora and other tools on 20-way dataset. A The average allelic recall and error rate curve for pandora, SAMtools, and snippy on 100× of Illumina data. Snippy/SAMtools both run 24 times with the different reference genomes shown in Fig. 4, resulting in multiple lines for each tool (one for each reference). B The average allelic recall and error rate curve for pandora, medaka, and nanopolish on 100× of Nanopore data; multiple lines for medaka/nanopolish, one for each reference genome. Note panels A and B have the same y-axis scale and limits, but different x axes. C The precision of pandora, SAMtools, and snippy on 100× of Illumina data. The boxplots show the distribution of SAMtools’ and snippy’s precision depending on which of the 24 references was used, and the blue line connects pandora’s results. D The precision of pandora (line plot), medaka, and nanopolish (both boxplots) on 100× of Nanopore data. Note different y-axis scale/limits in panels C and D