Table 4.
Error rates after alignment of patched and corrected reads against the respective reference genome using blasr
| unpatched | MARVEL patched | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Consensus correction | None | Canu MHAP | Canu minimap2 | Proovread | None | MARVEL | Canu MHAP | Canu minimap2 | Proovread |
| ONT | ONT | ||||||||
| Substitution % | 3.50 | 0.20 | 0.19 | 0.25 | 3.19 | 0.21 | 0.17 | 0.16 | 0.10 |
| Insertion % | 4.01 | 0.19 | 0.18 | 0.22 | 3.81 | 0.26 | 0.17 | 0.16 | 0.10 |
| Deletion % | 4.94 | 1.65 | 1.67 | 0.78 | 4.21 | 0.89 | 1.25 | 1.21 | 0.25 |
| Total error % | 12.45 | 2.04 | 2.04 | 1.25 | 11.21 | 1.36 | 1.59 | 1.53 | 0.45 |
| Longest perfect match (bp) | 369 | 1694 | 1845 | 84 881 | 369 | 1275 | 1819 | 1833 | 92 302 |
| PacBio | PacBio | ||||||||
| Substitution % | 1.07 | 0.08 | 0.07 | 0.15 | 0.93 | 0.05 | 0.08 | 0.07 | 0.08 |
| Insertion % | 8.33 | 0.30 | 0.22 | 1.19 | 7.22 | 0.35 | 0.28 | 0.17 | 0.55 |
| Deletion % | 3.43 | 0.26 | 0.24 | 0.23 | 3.02 | 0.21 | 0.26 | 0.18 | 0.09 |
| Total error % | 12.83 | 0.64 | 0.53 | 1.57 | 11.15 | 0.61 | 0.62 | 0.42 | 0.72 |
| Longest perfect match (bp) | 191 | 14 682 | 14 756 | 33 315 | 191 | 4398 | 18 450 | 12 712 | 39 811 |