Comparison of taxonomic profiling methods on HMP mock community data.

We compared the four tools MetaPhlAn, mOTUs, Pathoscope, and MicrobeGPS. For Pathoscope and MicrobeGPS, we used two different reference genome sets, HMP and NCBI (see text). For each tool, we report the overall precision and sensitivity with respect to the ground truth. The maximum F-measure and the area under the ROC curve (AUC) were calculated comparing the N most abundant identifications to the ground truth. Highest scores are written in bold font. For Pathoscope, we manually applied a relative abundance cutoff of 10−5.