Table 3 The MetaBenchmark performance metrics for ten metagenomics analysis tools at phylum level
Tool | Precision | Sensitivity | Specificity | NPV | MCC | Run time |
|---|---|---|---|---|---|---|
UMGAP tryptic precision | 100.00% | 6.10% | 100.00% | 21.03% | 11.32% | 7.27 min |
Kraken | 99.98% | 88.95% | 99.92% | 69.35% | 78.49% | 223.16 min |
UMGAP max precision | 99.99% | 73.50% | 99.96% | 48.55% | 59.71% | 17.08 min |
Kraken 2 | 99.99% | 91.08% | 99.97% | 73.70% | 81.91% | 2.14 min |
UMGAP high precision | 99.96% | 83.02% | 99.88% | 59.56% | 70.25% | 31.74 min |
Kaiju | 99.96% | 84.32% | 99.88% | 61.47% | 71.92% | 317.04 min |
UMGAP tryptic sensitivity | 99.69% | 30.77% | 99.62% | 26.55% | 28.24% | 6.40 min |
UMGAP high sensitivity | 94.72% | 93.35% | 83.48% | 79.83% | 75.68% | 31.85 min |
UMGAP max sensitivity | 81.50% | 100.00% | 37.88% | 100.00% | 55.56% | 32.52 min |
CLARK | 74.28% | 100.00% | 7.87% | 100.00% | 24.17% | 22.39 min |