Fig. 2

Evaluation of mOTU profiling on simulated samples. Benchmarks of quantification accuracy (a–g) on ten simulated metagenomic samples (Methods) containing MAGs with (n = 50) and MAGs without (n = 50) a representative reference genome sequence, (h–o) and the CAMI challenge datasets²⁵. a–d A representative simulated metagenome (out of ten; Supplementary Figures 8, 9) analysed with four profilers. e Precision-recall plot, where each data point corresponds to one of the ten simulated samples. Mean absolute error (MAE, also referred to as L1 norm) (f) and differences of the Shannon diversity index (g) from the expected values (error bars in f and g show standard deviation). h–j Average precision-recall values over the two medium complexity samples and (l–n) average precision-recall values over the five high complexity samples of the CAMI dataset (see also Supplementary Figure 10). Each precision-recall plot contains five values for mOTUs2, which correspond to different sets of parameters: high precision (-l 140 -g 6), default (-l 100 -g 3), recall (-l 75 -g 3), high recall (-l 50 -g 2) and maximum recall (-l 30 -g 1), indicating the versatility of mOTUs2 in optimising precision or recall. In (k) and (o), mean absolute errors (MAE; referred to as L1-norm in CAMI) at different taxonomic ranks are shown for several tools. For mOTUs2, results for two options of calculating relative abundances are shown: one with relative abundances re-normalized based on detected taxa, which is enforced in the CAMI evaluation (but artificially deteriorates quantification accuracy), and one without this additional re-normalization (see main text and Supplementary Figure 11 for details). Data are provided in Supplementary Data 3, 4. Other taxonomic profilers (MetaPhyler, TIPP, Taxy-Pro, FOCUS, CLARK, Quickr) evaluated in CAMI²⁵ are denoted by grey dots. Source data are provided as a Source Data file.