Fig. 2

Results of ReporTree benchmarking of the cg/wgMLST workflow using datasets for four different species: L. monocytogenes (Lm), S. enterica (Se), E. coli (Ec), and C. jejuni (Cj). A ReporTree running times for the 10 replicates of each subset of L. monocytogenes (top left), S. enterica (top right), E. coli (bottom left), and C. jejuni (bottom right), where the flag “all” indicates subsets for which ReporTree obtained clusters at all possible thresholds, the flag “outbreak” indicates subsets for which ReporTree obtained clusters at potential outbreak level (7 allelic differences for L. monocytogenes, 14 (0.43%) for S. enterica, 9 (0.34%) for E. coli, and 6 for (0.59%) for C. jejuni [14, 38]), and the flag “stability” indicates subsets for which ReporTree obtained clusters at all possible thresholds but only generated reports for those corresponding to stability regions. B Number of clusters generated at all possible distance thresholds for each dataset. C Comparison of running times when ReporTree obtained clusters at potential outbreak level