Table 3 Sensitivity, precision, and F1-score of the pathogen detection tools on a mock metagenomic dataset
From: MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data
Dataset | Spiked Bacteria | MegaPath | Centrifuge | CLARK | Kraken | Kraken2 |
|---|---|---|---|---|---|---|
| Â | Â | F1-score (Sensitivity, Precision) | ||||
1 | Enterococcus hirae | 98.5% (97.1, 99.9%) | 96.2% (92.8, 99.9%) | 98.0% (96.1, 100%) | 97.3% (94.8, 99.9%) | 97.7% (95.6, 99.9%) |
2 | Corynebacterium halotolerans | 98.5% (97.1, 100%) | 96.3% (92.8, 100%) | 98.0% (96.1, 100%) | 97.3% (94.8, 100%) | 97.8% (95.6, 100%) |
3 | Clostridium botulinum | 98.5% (97.1, 100%) | 96.3% (92.8, 99.9%) | 98.0% (96.1, 100%) | 97.3% (94.8, 100%) | 97.8% (95.6, 99.9%) |
4 | Corynebacterium falsenii | 98.5% (97.1, 100%) | 96.3% (92.8, 100%) | 98.0% (96.1, 100%) | 97.3% (94.8, 100%) | 97.8% (95.6, 100%) |
5 | Gardnerella vaginalis | 98.6% (97.2, 100%) | 96.3% (92.9, 100%) | 98.0% (96.1, 100%,) | 97.3% (94.8, 100%) | 97.8% (95.7, 100%) |
6 | Pasteurella multocida | 98.6% (97.2, 100%) | 96.3% (92.9, 100%) | 98.0% (96.1, 100%) | 97.3% (94.8, 100%) | 97.8% (95.7, 100%) |
7 | Micrococcus luteus | 98.6% (97.2, 100%) | 96.4% (93.0, 100%) | 98.1% (96.2, 100%) | 97.4% (94.9, 100%) | 97.8% (95.8, 100%) |
8 | Gallibacterium anatis | 98.6% (97.3, 100%) | 96.4% (93.0, 100%) | 98.1% (96.2, 100%) | 97.4% (95.0, 100%) | 97.8% (95.8, 100%) |
9 | Citrobacter freundii | 98.5% (97.2, 99.9%) | 96.4% (93.0, 99.9%) | 98.0% (96.2, 99.9%) | 97.4% (95.0, 99.9%) | 97.8% (95.8, 99.9%) |
10 | Haemophilus parainfluenzae | 98.6% (97.3, 100%) | 96.4% (93.0, 99.9%) | 98.1% (96.3, 100%) | 97.4% (95.0, 100%) | 97.8% (95.8, 100%) |
11 | Leuconostoc gasicomitatum | 98.2% (96.6, 100%) | 96.4% (93.0, 99.9%) | 98.1% (96.3, 100%) | 97.4% (95.0, 100%) | 97.9% (95.8, 100%) |
12 | Human campylobacteriosis | 98.6% (97.3, 100%) | 96.4% (93.0, 100%) | 98.1% (96.3, 100%) | 97.4% (95.0, 100%) | 97.8% (95.8, 100%) |