Table 3.

Abundance estimation performance results on a simulated fungal community consisting of 40 genomes derived from 7 different species

	L1 error	Precision	Recall/Sensitivity	F1-Score
MiCoP	0.00017	1.0	1.0	1.0
Kraken	0.01420*	1.0	0.83333	0.90909
MetaPhlAn2	0.00924	0.85714	1.0	0.92308

These species were sampled in the same way as in the previous table: by taking the intersect of species detected by all three tools on a higher-complexity community. MiCoP detected the exact set of species present in the sample, while Kraken had one false negative and MetaPhlAn had one false positive. Additionally, MiCoP’s abundance estimation was more than an order of magnitude better than the other tools. * Based on read classification proportions; Kraken does not claim to perform abundance estimation