Table 2:
Benchmarking SV recall, precision, and F1 on HG002 Human (hg19) PacBio reads (CLR and HiFi) at varying coverages (CLR 10×, 20×, 30×; HiFi 10×)
| Method | Recall, % | Precision, % | F1, % |
|---|---|---|---|
| PacBio CLR 10× | |||
| minimap2 | 62.85 | 88.88 | 73.63 |
| NGMLR | 60.11 | 86.44 | 70.91 |
| Vulcan | |||
| 60% | 60.13 | 89.41 | 71.90 |
| 70% | 60.79 | 90.12 | 72.61 |
| 80% | 60.97 | 90.13 | 72.73 |
| 90% | 61.85 | 89.93 | 73.29 |
| PacBio CLR 20× | |||
| minimap2 | 77.76 | 71.85 | 74.69 |
| NGMLR | 75.74 | 68.36 | 71.86 |
| Vulcan | |||
| 60% | 75.74 | 74.69 | 75.21 |
| 70% | 75.98 | 75.32 | 75.65 |
| 80% | 76.22 | 75.65 | 75.93 |
| 90% | 76.90 | 75.08 | 75.98 |
| PacBio CLR 30× | |||
| minimap2 | 83.71 | 86.25 | 84.96 |
| NGMLR | 81.79 | 82.41 | 82.10 |
| Vulcan | |||
| 60% | 82.05 | 86.31 | 84.12 |
| 70% | 82.33 | 87.12 | 84.66 |
| 80% | 82.47 | 87.60 | 84.96 |
| 90% | 82.75 | 87.49 | 85.05 |
| PacBio HiFi 10× | |||
| minimap2 | 81.50 | 90.70 | 85.85 |
| NGMLR | 78.22 | 86.26 | 82.04 |
| Vulcan | |||
| 60% | 77.73 | 86.04 | 81.68 |
| 70% | 77.74 | 86.19 | 81.75 |
| 80% | 76.40 | 85.75 | 80.81 |
| 90% | 76.26 | 85.73 | 80.72 |
Various percentile cut-offs for Vulcan were used, including 60%, 70%, 80%, 90%. Vulcan achieves the highest F1 score on PacBio CLR 20× and 30× reads, with minimap2 achieving the highest F1 score on PacBio CLR 10× and PacBio HiFi 10× reads.