Comparison of bacterial compositions estimated from different approaches. We have created a simulated metagenomic sample (Table 2) with 100bp reads to evaluate the performance of different approaches in estimating the bacterial compositions. ”16S Ideal” and ”Shotgun Ideal” represent results obtained by analyzing 16S rRNA genes and whole genome shotgun sequences assuming the classification accuracy is perfect. Genus ”Other” indicates that sequences have been classified into genera other than that in the simulated sample. Different approaches are ranked by their correlation coefficients (shown in legend) between the estimated and true taxonomic profile. When running MetaPhyler, the genomes from which the reads were simulated are removed from the reference database.