Table 1.
Verkko2 Hi-C versus trio benchmarking
| Sheep | Chicken | HG002 | HG00733 | |
|---|---|---|---|---|
| T2T scf | ||||
| Hi-C | 31 | 34 | 40 | 41 |
| Trio | 23 | 32 | 32 | 33 |
| T2T ctg | ||||
| Hi-C | 24 | 21 | 21 | 26 |
| Trio | 20 | 25 | 22 | 23 |
| Hamming error | ||||
| Hi-C | 0.85% | 0.58% | 0.39% | 0.75% |
| Trio | 0.88% | 0.60% | 0.39% | 0.77% |
| Switch error | ||||
| Hi-C | 0.95% | 0.13% | 0.41% | 0.79% |
| Trio | 0.95% | 0.13% | 0.41% | 0.79% |
| QV | ||||
| Hi-C | 54.17 | 45.13 | 53.87 | 53.86 |
| Trio | 54.17 | 45.17 | 53.89 | 53.82 |
| Missing genes | ||||
| Hi-C | 1.37% | 3.12% | 1.61% | 0.09% |
| Trio | 1.36% | 2.52% | 1.60% | 0.09% |
| Missing genes (no sex chrs) | ||||
| Hi-C | 0.06% | 1.06% | 0.09% | 0.09% |
| Trio | 0.06% | 0.44% | 0.09% | 0.09% |
| Dup genes | ||||
| Hi-C | 1.73% | 0.12% | 0.68% | 0.71% |
| Trio | 1.72% | 0.22% | 0.69% | 0.72% |
-
T2T contigs/scaffolds were counted as those >5 Mb with telomeres on both ends. Scaffolds were broken into contigs at any stretch of more than three N's, and contigs/scaffolds <100 kb were discarded for all metrics. Verkko Hi-C shows comparable QV, switch, hamming, and missing gene stats to Verkko trio, but it consistently has a higher count of T2T scaffolds owing to its ability to restore missing connectivity using Hi-C links. Bold text indicates the best score for each metric and species; ties are also bolded.
