Supplementary Figure 6: HUMAnN2 compared with other methods: synthetic metatranscriptome evaluation.

We profiled a 10-million-read synthetic gut metatranscriptome using HUMAnN2 (tiered and pure translated search modes), HUMAnN1, COGNIZER, MEGAN, and ShotMAP to produce profiles of community-level COG transcript abundance. Twenty species’ genomic abundance values were geometrically staggered (as in the gut metagenome evaluation), while genes (transcripts) were sampled within-species following a log-normal distribution [ln N(0, 1)]. (a) Measures of methods’ accuracy and performance in this evaluation. All methods were allowed to use 8 CPU cores and up to 30 GB of memory. This panel is analogous to Fig. 1e (which focuses on metagenomic COG abundance in the same synthetic community). (b) Observed versus expected COG transcript abundance across the six methods. This panel is analogous to Supplementary Fig. 4. CPM refers to “copies per million.” Ticks in the x- and y-axis margins represent zero values; x-axis ticks are false negatives and y-axis ticks are false positives