Table 2.
The MetaBenchmark performance metrics for ten metagenomics analysis tools at genus level
| Tool | Precision | Sensitivity | Specificity | NPV | MCC | Run time |
|---|---|---|---|---|---|---|
| UMGAP tryptic precision | 99.87% | 5.19% | 99.97% | 20.97% | 10.37% | 7.29 min |
| Kraken | 99.59% | 87.78% | 98.60% | 67.39% | 76.07% | 227.99 min |
| UMGAP max precision | 99.56% | 63.49% | 98.89% | 40.86% | 50.22% | 17.28 min |
| Kraken 2 | 98.64% | 89.10% | 95.40% | 70.02% | 76.17% | 2.15 min |
| UMGAP high precision | 99.08% | 73.24% | 97.40% | 48.63% | 58.05% | 31.59 min |
| Kaiju | 99.04% | 80.49% | 97.02% | 56.51% | 65.62% | 314.55 min |
| UMGAP tryptic sensitivity | 98.14% | 25.62% | 98.12% | 25.36% | 23.62% | 6.37 min |
| UMGAP high sensitivity | 93.78% | 85.81% | 82.38% | 65.20% | 63.42% | 31.83 min |
| UMGAP max sensitivity | 81.58% | 100.00% | 54.58% | 100.00% | 66.72% | 32.41 min |
| CLARK | 70.76% | 100.00% | 8.97% | 100.00% | 25.19% | 22.27 min |