Table 1.
Performance of Causalcall, Chiron v0.4.2 (DNAde), Chiron v0.4.2 (DNAre), Guppy v3.1.5, and Flappie v1.1.0 on the four testing sets.
| Species | Basecaller | Deletion (%) | Insertion (%) | Mismatch (%) | Identity (%) | Error (%) | Speed (bps) |
|---|---|---|---|---|---|---|---|
| Lambda phage | Causalcall | 6.48 | 1.84 | 4.30 | 89.21 | 12.62 | 7385 |
| Chiron (DNAde) | 8.20 | 2.27 | 5.77 | 86.03 | 16.24 | 2568 | |
| Chiron (DNAre) | 6.86 | 2.22 | 4.71 | 88.43 | 13.79 | 2721 | |
| Guppy | 4.60 | 2.02 | 3.00 | 92.40 | 9.62 | 379883 | |
| Flappie | 5.01 | 2.28 | 3.50 | 91.50 | 10.79 | 9398 | |
| E. coli | Causalcall | 5.95 | 2.07 | 4.57 | 89.48 | 12.59 | 7172 |
| Chiron (DNAde) | 7.07 | 2.47 | 6.04 | 86.89 | 15.58 | 2485 | |
| Chiron (DNAre) | 5.91 | 2.34 | 4.65 | 89.44 | 12.90 | 2761 | |
| Guppy | 4.06 | 1.97 | 3.02 | 92.92 | 9.05 | 363389 | |
| Flappie | 4.60 | 2.28 | 3.60 | 91.79 | 10.48 | 6678 | |
| Human | Causalcall | 8.06 | 2.27 | 5.06 | 86.88 | 15.39 | 6548 |
| Chiron (DNAde) | 8.49 | 2.92 | 5.41 | 86.10 | 16.82 | 2045 | |
| Chiron (DNAre) | 7.76 | 2.98 | 5.56 | 86.68 | 16.30 | 1992 | |
| Guppy | 4.78 | 2.46 | 2.86 | 92.35 | 10.10 | 349665 | |
| Flappie | 5.33 | 2.67 | 3.35 | 91.32 | 11.35 | 7212 | |
| K. pneumoniae | Causalcall | 5.58 | 4.82 | 6.29 | 88.12 | 16.69 | 6657 |
| Chiron (DNAde) | 5.70 | 6.41 | 7.92 | 86.38 | 20.03 | 2540 | |
| Chiron (DNAre) | 5.13 | 6.26 | 6.9 | 87.98 | 18.29 | 2446 | |
| Guppy | 4.10 | 4.16 | 4.49 | 91.41 | 12.75 | 305153 | |
| Flappie | 5.06 | 4.26 | 5.42 | 89.52 | 14.74 | 6400 |
1
Chiron (DNAde) and Chiron (DNAre) represent the default and the retrained Chiron, respectively.
Identify rate of the mapping is the metric for basecalling accuracy [the higher the better, identify rate = 1 – (deletion rate + mismatch rate)]. Error rate is calculated by summing the rates of deletion, insertion, and mismatch (the lower the better).