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Table 2 Performance of KrakenUniq (with unique k-mer count thresholds) compared to metagenomics classifiers [15] on the biological datasets (n = 10). F1 and recall show the average values over the datasets. Note that “KrakenUniq reads” would be equivalent to standard Kraken

From: KrakenUniq: confident and fast metagenomics classification using unique k-mer counts

  Genus Species  
F1 Recall F1 Recall Avg
KrakenUniq nt k-mers 0.99 0.99 0.99 0.98 0.99
KrakenUniq nt reads 0.96 0.91 0.97 0.95 0.95
BlastMeganFilteredLiberal 0.97 0.94 0.97 0.89 0.94
BlastMeganFiltered 0.97 0.93 0.96 0.87 0.93
KrakenUniq orig k-mers 0.96 0.93 0.94 0.87 0.93
ClarkM4Spaced 0.95 0.90 0.94 0.88 0.92
KrakenUniq orig reads 0.95 0.90 0.94 0.85 0.91
Kraken 0.95 0.90 0.94 0.84 0.91
KrakenUniq std. k-mers 0.97 0.94 0.92 0.78 0.90
DiamondMegan_sensitive 0.98 0.93 0.92 0.74 0.89
KrakenFiltered 0.95 0.91 0.90 0.75 0.88
ClarkM1Default 0.94 0.85 0.91 0.77 0.87
KrakenUniq std. reads 0.95 0.89 0.90 0.70 0.86
LMAT 0.97 0.93 0.91 0.60 0.85
DiamondMegan 0.94 0.87 0.91 0.66 0.85
Gottcha 0.91 0.84 0.87 0.67 0.82
NBC 0.87 0.76 0.85 0.73 0.80
Metaphlan 0.94 0.89 0.83 0.55 0.80
MetaFlow 0.66 0.53 0.65 0.51 0.59
PhyloSift 0.68 0.29 0.78 0.54 0.57
PhyloSift90pct 0.68 0.30 0.77 0.52 0.57
  1. Bold values indicate the highest value in each column