Fig. 3
From: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
Combining results from imprecise tools can predict the true number of species in a dataset. a UpSet plots of the top-X (by abundance) species uniquely found by a classifier or group of classifiers (grouped by black dots at bottom, unique overlap sizes in the bar charts above). The eval_RAIphy dataset is presented as an example, with comparison sizes X = 25 and X = 50. The percent overlap, calculated as the number of species overlapping between all tools, divided by the number of species in the comparison, increases around the number of species in the sample (50 in this case). b The percent overlaps for all datasets show a similar trend. c The rightmost peak in (b) approximates the number of species in a sample, with a root mean square error (RMSE) of 8.9 on the test datasets. d Precise tools can offer comparable or better estimates of species count. RMSE = 3.2, 3.8, 3.9, 12.2, and 32.9 for Kraken filtered, BlastMegan filtered, GOTTCHA, Diamond-MEGAN filtered, and MetaPhlAn2, respectively