Table 2.

Performance metrics for Kraken, Centrifuge, RFPlasmid, mlplasmids, PlaScope and Platon on contigs from 82 KpSC genomes

	Kraken	Centrifuge	RFPlasmid	mlplasmids	PlaScope	Platon
Sensitivity (true positive rate, %)
Contig length	96.507	94.565	94.198	95.987	87.199	80.215
Contig count	90.796	90.485	82.898	95.833	81.157	74.192
Specificity (true negative rate, %)
Contig length	99.973	99.941	99.859	99.727	99.958	99.984
Contig count	99.378	99.189	98.458	91.804	99.243	99.405
Precision (positive predictive value, %)
Contig length	99.472	98.851	97.289	94.965	99.120	99.638
Contig count	98.449	97.980	95.899	83.568	97.899	98.189
Negative predictive value (%)
Contig length	99.813	99.709	99.689	99.784	99.317	98.948
Contig count	96.128	95.995	92.976	98.064	92.372	89.853
Accuracy (%)
Contig length	99.796	99.667	99.570	99.536	99.308	98.977
Contig count	96.777	96.550	93.742	93.025	93.761	91.762
F1-score (%)
Contig length	97.967	96.660	95.719	95.474	92.778	88.878
Contig count	94.468	94.083	88.926	89.282	88.745	84.520

Total contig sizes and contig counts assigned to each category (true positive, true negative, false positive and false negative) are provided in Table S3. Bold font indicates the highest value in each category.