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Table 2 Abundance estimation performance results on a simulated viral community with 40 species

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

  L1 error Precision Recall/Sensitivity F1-Score
MiCoP 0.00909 1.0 1.0 1.0
Kraken 1.15466* 0.82222 0.925 0.87059
MetaPhlAn2 0.09844 1.0 1.0 1.0
  1. These species were sampled from the intersect of the species detected by all three tools in the previous simulation. Thus, this simulation consisted of only the species that were present in all three reference databases, eliminating reference bias. MetaPhlAn’s performance dramatically improved, predicting the exact set of species in the sample, but its abundance estimation was an order of magnitude worse than MiCoP’s. Kraken’s results did not markedly improve in this simulation. * Based on read classification proportions; Kraken does not claim to perform abundance estimation