Table 1. Ability of chimera.slayer, Uchime, and chimera.perseus to detect reliably chimeras within the sliding window and shhh.flows pipelines when using the Gold sequence collection or the dataset itself as the reference.
| Sequence curation pipeline | Chimera detection algorithm | Database | Sensitivitya , b | Specificity | False discovery rate | Initial % chimeras | Final % chimeras |
| Sliding window | chimera.slayer | Gold | 68.7 (11.8) | 95.0 (3.4) | 3.7 (3.4) | 67.8 (11.9) | 39.6 (8.4) |
| Self | 66.5 (11.8) | 94.2 (3.7) | 4.4 (4.1) | 67.8 (11.9) | 41.4 (9.3) | ||
| Uchime | Gold | 79.2 (8.0) | 93.7 (3.7) | 4.1 (3.3) | 67.8 (11.9) | 30.6 (8.7) | |
| Self | 74.5 (10.5) | 94.4 (3.7) | 4.0 (3.7) | 67.8 (11.9) | 34.6 (8.5) | ||
| chimera.perseus | Self | 76.0 (5.9) | 91.6 (5.0) | 5.6 (4.9) | 67.8 (11.9) | 34.8 (10.6) | |
| shhh.flows | chimera.slayer | Gold | 79.7 (7.7) | 95.9 (2.6) | 1.9 (1.2) | 71.8 (7.3) | 33.8 (13.2) |
| Self | 79.5 (7.1) | 94.4 (3.6) | 2.5 (1.4) | 71.8 (7.3) | 34.2 (12.3) | ||
| Uchime | Gold | 89.6 (6.3) | 93.7 (3.9) | 2.6 (1.7) | 71.8 (7.3) | 20.8 (11.3) | |
| Self | 87.3 (5.8) | 93.8 (4.0) | 2.6 (1.6) | 71.8 (7.3) | 24.5 (10.8) | ||
| chimera.perseus | Self | 87.4 (6.8) | 92.7 (4.3) | 2.9 (1.5) | 71.8 (7.3) | 24.4 (12.4) |
a
All values in this table were calculated using unique sequences.
b
The standard deviation is given in parentheses.