Fig. 4

The mean squared log error (MSLE) and the number of false positive taxa (FP) between true and estimated read counts at the levels of genus, species, and strain using reference 3. We measured MSLE (a) using unfiltered results (0 x axis tick) and (b) by removing all instances where the true and estimated counts were both zero (1 x axis tick). False positive taxa were counted at all read thresholds between 0 and 10. At the read threshold of 0 reads (unfiltered results), all taxa were counted, even those with just 1 assigned read. At the read threshold of 1 read, we counted the taxa with > 1 assigned read and so on. Bracken, MetaPhlAn 3, and Kaiju produce results up to the species level and thus they were not included in the strain-level comparisons. Smaller MSLE and smaller numbers of false positives denote better performance