Table 7.
F1 scores for species and genus detection of ATCC MSA-1003 mock community by 5 different algorithms
| Algorithm | Species | Genus | ||||
|---|---|---|---|---|---|---|
| F1 | Sensitivity | Precision | F1 | Sensitivity | Precision | |
| Minimap2 | 26.67 | 80.00 | 16.00 | 47.62 | 83.33 | 33.33 |
| Mora | 37.64 | 80.00 | 24.62 | 55.56 | 83.33 | 41.67 |
| AugPatho2 | 41.02 | 80.00 | 27.59 | 58.82 | 83.33 | 45.45 |
| Kraken2 | 55.38 | 90.00 | 40.00 | 65.31 | 88.90 | 51.61 |
| Bracken | 52.94 | 90.00 | 37.50 | 64.00 | 88.90 | 50.00 |
Kraken2 has the highest F1 score for both species and genus levels. Mora and AugPatho2 improve minimap2’s classifications, although their value is lower than Kraken2/Bracken