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Page 8 of 16 Pham et al. Microbiome Res Rep 2024;3:25 https://dx.doi.org/10.20517/mrr.2024.01

Table 1. Comparison of species identification on Mende and CAMI datasets
Dataset Sample Method Precision Recall F1-score
Mende 10 species MetaBIDx 1.000 0.800 0.889
CLARK 0.027 1.000 0.053
KrakenUniq 0.040 0.800 0.075
Kraken2 0.025 0.800 0.048
Centrifuge 0.021 0.800 0.041
Sourmash 0.900 0.900 0.900
100 species MetaBIDx 1.000 0.976 0.988
CLARK 0.236 1.000 0.382
KrakenUniq 0.234 0.713 0.352
Kraken2 0.222 0.760 0.345
Centrifuge 0.221 0.850 0.351
Sourmash 0.852 0.750 0.800
400 species MetaBIDx 1.000 0.970 0.985
CLARK 0.876 1.000 0.933
KrakenUniq 0.952 0.651 0.773
Kraken2 0.870 0.753 0.807
Centrifuge 0.876 0.883 0.879
Sourmash 0.837 0.849 0.843
CAMI RH_S001 MetaBIDx 0.862 0.449 0.591
CLARK 0.059 1.000 0.111
KrakenUniq 0.054 0.498 0.097
Kraken2 0.087 0.427 0.144
Centrifuge 0.058 0.536 0.104
Sourmash 0.286 0.539 0.374
RH_S002 MetaBIDx 0.843 0.677 0.751
CLARK 0.059 1.000 0.111
KrakenUniq 0.054 0.498 0.097
Kraken2 0.087 0.427 0.144
Centrifuge 0.058 0.536 0.104
Sourmash 0.287 0.550 0.377
RH_S003 MetaBIDx 0.885 0.689 0.774
CLARK 0.059 1.000 0.111
KrakenUniq 0.054 0.498 0.097
Kraken2 0.087 0.427 0.144
Centrifuge 0.058 0.536 0.104
Sourmash 0.274 0.550 0.366
RH_S004 MetaBIDx 0.839 0.778 0.807
CLARK 0.059 1.000 0.111
KrakenUniq 0.054 0.498 0.097
Kraken2 0.087 0.427 0.144
Centrifuge 0.058 0.536 0.104
Sourmash 0.296 0.550 0.385
RH_S005 MetaBIDx 0.854 0.737 0.791
CLARK 0.059 1.000 0.111
KrakenUniq 0.054 0.498 0.097
Kraken2 0.087 0.427 0.144