TABLE 2.
Performance on external datasets.
| Group | Measure | Read assignment |
VGAC ≥ 0.1 |
VGAC ≥ 0.3 |
80/80 |
Distance |
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| C | K | M | Ave | C | K | M | Ave | C | K | M | Ave | C | K | M | Ave | VGAC0.1 | VGAC0.3 | ||
| Viromock | Sensitivity | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.87 | 0.96 | 0.87 | 0.87 | 0.80 | 0.84 | 1.00 | 0.93 | 0.80 | 0.91 | 0.0943 | 0.1491 |
| Specificity | 0.24 | 0.24 | 0.86 | 0.44 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.0000 | 0.0000 | |
| Precision | 0.28 | 0.28 | 0.68 | 0.41 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.0000 | 0.0000 | |
| Accuracy | 0.41 | 0.41 | 0.89 | 0.57 | 1.00 | 1.00 | 0.97 | 0.99 | 0.97 | 0.97 | 0.95 | 0.96 | 1.00 | 0.98 | 0.95 | 0.98 | 0.0214 | 0.0339 | |
| FDR | 0.72 | 0.72 | 0.32 | 0.59 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.0000 | 0.0000 | |
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| SmallRNA | Sensitivity | 1.00 | 0.77 | 0.77 | 0.85 | 0.50 | 0.45 | 0.36 | 0.44 | 0.27 | 0.32 | 0.18 | 0.26 | 0.27 | 0.23 | 0.14 | 0.21 | 0.3936 | 0.1016 |
| Specificity | 0.33 | 0.50 | 0.92 | 0.58 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.0000 | 0.0000 | |
| Precision | 0.73 | 0.74 | 0.94 | 0.81 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.0000 | 0.0000 | |
| Accuracy | 0.76 | 0.68 | 0.82 | 0.75 | 0.68 | 0.65 | 0.59 | 0.64 | 0.53 | 0.56 | 0.47 | 0.52 | 0.53 | 0.50 | 0.44 | 0.49 | 0.2547 | 0.0658 | |
| FDR | 0.27 | 0.26 | 0.06 | 0.19 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.0000 | 0.0000 | |
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| Nanopore | Sensitivity | 0.96 | 0.96 | 0.96 | 0.96 | 0.96 | 0.96 | 0.96 | 0.96 | 0.92 | 0.92 | 0.92 | 0.92 | 0.96 | 0.96 | 0.92 | 0.95 | 0.0385 | 0.0544 |
| Specificity | 0.22 | 0.33 | 0.67 | 0.41 | 1.00 | 1.00 | 0.94 | 0.98 | 1.00 | 1.00 | 0.94 | 0.98 | 1.00 | 1.00 | 0.94 | 0.98 | 0.0000 | 0.0000 | |
| Precision | 0.64 | 0.68 | 0.81 | 0.71 | 1.00 | 1.00 | 0.96 | 0.99 | 1.00 | 1.00 | 0.96 | 0.99 | 1.00 | 1.00 | 0.96 | 0.99 | 0.0015 | 0.0000 | |
| Accuracy | 0.66 | 0.70 | 0.84 | 0.73 | 0.98 | 0.98 | 0.95 | 0.97 | 0.95 | 0.95 | 0.93 | 0.95 | 0.98 | 0.98 | 0.93 | 0.96 | 0.0227 | 0.0321 | |
| FDR | 0.36 | 0.32 | 0.19 | 0.29 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.0015 | 0.0000 | |
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| Average All | Sensitivity | 0.99 | 0.91 | 0.91 | 0.94 | 0.82 | 0.81 | 0.73 | 0.79 | 0.69 | 0.70 | 0.63 | 0.68 | 0.74 | 0.71 | 0.62 | 0.69 | 0.1662 | 0.0594 |
| Specificity | 0.26 | 0.36 | 0.82 | 0.48 | 1.00 | 1.00 | 0.98 | 0.99 | 1.00 | 1.00 | 0.98 | 0.99 | 1.00 | 1.00 | 0.98 | 0.99 | 0.0000 | 0.0000 | |
| Precision | 0.55 | 0.56 | 0.81 | 0.64 | 1.00 | 1.00 | 0.99 | 1.00 | 1.00 | 1.00 | 0.99 | 1.00 | 1.00 | 1.00 | 0.99 | 1.00 | 0.0005 | 0.0000 | |
| Accuracy | 0.61 | 0.60 | 0.85 | 0.69 | 0.88 | 0.87 | 0.84 | 0.87 | 0.82 | 0.83 | 0.79 | 0.81 | 0.84 | 0.82 | 0.78 | 0.81 | 0.0955 | 0.0214 | |
| FDR | 0.45 | 0.44 | 0.19 | 0.36 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.0005 | 0.0000 | |
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| Average Viromock + Nanopore | Sensitivity | 0.98 | 0.98 | 0.98 | 0.98 | 0.98 | 0.98 | 0.91 | 0.96 | 0.89 | 0.89 | 0.86 | 0.88 | 0.98 | 0.95 | 0.86 | 0.93 | 0.0622 | 0.1007 |
| Specificity | 0.23 | 0.28 | 0.76 | 0.43 | 1.00 | 1.00 | 0.97 | 0.99 | 1.00 | 1.00 | 0.97 | 0.99 | 1.00 | 1.00 | 0.97 | 0.99 | 0.0000 | 0.0000 | |
| Precision | 0.46 | 0.48 | 0.74 | 0.56 | 1.00 | 1.00 | 0.98 | 0.99 | 1.00 | 1.00 | 0.98 | 0.99 | 1.00 | 1.00 | 0.98 | 0.99 | 0.0008 | 0.0000 | |
| Accuracy | 0.53 | 0.56 | 0.87 | 0.65 | 0.99 | 0.99 | 0.96 | 0.98 | 0.96 | 0.96 | 0.94 | 0.96 | 0.99 | 0.98 | 0.94 | 0.97 | 0.0204 | 0.0326 | |
| FDR | 0.54 | 0.52 | 0.26 | 0.44 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.0008 | 0.0000 | |
Refer to “Materials and methods” for more details on these measures. Distance between measures of VGAC and 80/80 schema. For a full disclosure of these data, refer to Supplementary Table 10. C, Centrifuge; K, Kraken2; M, Minimap2; Ave, Average value. The average values are indicated in bold.