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Table 3 Abundance estimation performance results on a simulated fungal community consisting of 40 genomes derived from 7 different species

From: MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples

  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
  1. 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