Supplementary Figure 4: HUMAnN2 compared with other methods (details).

We profiled a 10-million-read synthetic gut metagenome using HUMAnN2 (tiered and pure translated search modes), HUMAnN1, COGNIZER, MEGAN, and ShotMAP to produce profiles of COG abundance. Here, expected (gold standard) and observed COG abundances are compared in units of copies per million (CPMs; that is., raw abundance normalized by gene length and number of mapped reads). HUMAnN2′s tiered search was considerably more accurate than the other methods based on pure translated search. HUMAnN2′s pure translated search showed better agreement than other translated search methods, with its largest source of error being underreporting of low-abundance COGs (false negatives). This behavior is expected from the translated search coverage filters used in HUMAnN2, which we use to limit false positive detection events (that is., COGs with zero expected abundance and non-zero observed abundance). Ticks in the x- and y-axis margins represent zero values; x-axis ticks are false negatives and y-axis ticks are false positives