TABLE 1.
Benchmark of Kraken's precision and sensitivity for isolates of Shigella spp.
| Isolate | Species identified by culture | Phyletic lineagea | No. of reads (Mb) | Estimated coverage | Precision or sensitivity (%)b |
|||
|---|---|---|---|---|---|---|---|---|
| Genus precision | Genus sensitivity | Species precision | Species sensitivity | |||||
| PK1010072 | S. flexneri | S1 | 4.3 | 95.8 | 86.8 | 38.4 | 2.3 | 0.8 |
| PK1010893 | S. flexneri | S1 | 9.6 | 214.1 | 86.7 | 37.4 | 2.4 | 0.9 |
| PK1011266 | S. boydii | S1 | 10.4 | 231.5 | 87.4 | 39.3 | 2.4 | 0.9 |
| PK1010319 | S. flexneri | S1 | 16.4 | 364.8 | 88.7 | 40.0 | 82.7 | 30.4 |
| PK1010319 | S. sonnei | S2 | 6.5 | 144.1 | 96.9 | 36.0 | 95.1 | 28.3 |
| PK1010339 | S. flexneri | S5 | 5.1 | 112.6 | 96.2 | 50.6 | 93.4 | 40.5 |
| PK1010355 | S. flexneri | S5 | 7.0 | 154.6 | 99.2 | 54.1 | 98.7 | 43.8 |
| PK1010912 | S. flexneri | S5 | 10.1 | 224.3 | 94.0 | 46.7 | 92.9 | 38.9 |
| PK1010943 | S. flexneri | S5 | 3.1 | 69.0 | 95.1 | 47.6 | 92.2 | 40.0 |
| PK1010438 | S. flexneri | S5 | 14.4 | 320.8 | 91.5 | 45.9 | 88.7 | 38.4 |
| PK1011037 | S. flexneri | S5 | 9.7 | 215.7 | 95.8 | 47.9 | 93.4 | 40.4 |
| PK1011283 | S. flexneri | S5 | 10.4 | 230.0 | 99.1 | 53.5 | 98.6 | 43.6 |
a
Phyletic lineage was assigned according to the system of Sahl et al. (20).
b
Sensitivity refers to the proportion of sequences assigned to the correct Shigella genus or species. Precision, i.e., the positive predictive value, refers to the proportion of correct classifications, out of the total number of classifications attempted.