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Page 10 of 16 Pham et al. Microbiome Res Rep 2024;3:25 https://dx.doi.org/10.20517/mrr.2024.01

Table 2. Comparison of species identification based on approximate coverage on Mende and CAMI datasets
Dataset Sample Method Precision Recall F1-score
Mende 10 species MetaBIDx 1.000 0.800 0.889
CLARK 1.000 0.800 0.889
KrakenUniq 1.000 0.800 0.889
Kraken2 1.000 0.700 0.824
Centrifuge 0.471 0.800 0.593
100 species MetaBIDx 1.000 0.976 0.988
CLARK 0.988 0.859 0.919
KrakenUniq 0.982 0.644 0.778
Kraken2 0.985 0.670 0.798
Centrifuge 0.790 0.830 0.810
400 species MetaBIDx 1.000 0.970 0.985
CLARK 0.990 0.965 0.977
KrakenUniq 0.989 0.634 0.773
Kraken2 0.987 0.733 0.841
Centrifuge 0.949 0.882 0.915
CAMI RH_S001 MetaBIDx 0.862 0.449 0.591
CLARK 0.688 0.515 0.589
KrakenUniq 0.673 0.258 0.373
Kraken2 0.699 0.238 0.356
Centrifuge 0.624 0.275 0.382
RH_S002 MetaBIDx 0.843 0.677 0.751
CLARK 0.650 0.868 0.744
KrakenUniq 0.640 0.427 0.512
Kraken2 0.630 0.384 0.477
Centrifuge 0.520 0.480 0.499
RH_S003 MetaBIDx 0.885 0.689 0.774
CLARK 0.670 0.814 0.735
KrakenUniq 0.674 0.393 0.497
Kraken2 0.667 0.377 0.482
Centrifuge 0.621 0.417 0.499
RH_S004 MetaBIDx 0.839 0.778 0.807
CLARK 0.661 0.910 0.766
KrakenUniq 0.637 0.458 0.533
Kraken2 0.610 0.394 0.479
Centrifuge 0.580 0.467 0.517
RH_S005 MetaBIDx 0.854 0.737 0.791
CLARK 0.677 0.814 0.739
KrakenUniq 0.676 0.403 0.505
Kraken2 0.651 0.364 0.467
Centrifuge 0.578 0.444 0.502
RM_S001 MetaBIDx 0.821 0.397 0.535
CLARK 0.686 0.414 0.516
KrakenUniq 0.611 0.247 0.352
Kraken2 0.577 0.169 0.261
Centrifuge 0.558 0.270 0.364
RM_S002 MetaBIDx 0.941 0.276 0.427