Table 3.
Benchmarking results for ONT data
| Dataset | Assembler | Size (Mb) | HC (%) | k-mer recovery(%) | Continuity (bp) | QV | Switch error(%) | N (%) | Dup (%) | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| All | Mat | Pat | NG50 | NGA50 | Phased N50 | ||||||||
| MHC (ONT 25x) | phasebook | 14.5 | 97.0 | 98.4 | 94.0 | 87.7 | 152,599 | 152,599 | 102,954 | 36.9 | 0.78 | 0.0 | 1.82 |
| phasebook-hi | 14.8 | 91.6 | 97.5 | 89.4 | 88.8 | 796,423 | 746,361 | 176,895 | 40.6 | 6.99 | 0.0 | 1.96 | |
| Canu | 5.9 | 59.6 | 95.4 | 83.2 | 65.9 | 1,419,330 | 93,217 | 100,918 | 33.4 | 6.44 | 0.0 | 0.84 | |
| Falcon | 6.3 | 67.8 | 94.3 | 82.2 | 68.8 | 2,489,921 | 442,832 | 220,087 | 27.6 | 4.65 | 0.0 | 1.10 | |
| Flye | 5.0 | 54.5 | 95.0 | 81.4 | 62.6 | 792,993 | 86,893 | 106,195 | 39.7 | 6.22 | 0.0 | 0.82 | |
| Shasta | 5.0 | 63.0 | 86.8 | 62.5 | 48.5 | 957,250 | 136,119 | 147,280 | 23.7 | 10.71 | 0.0 | 0.89 | |
| Wtdbg2 | 5.0 | 76.5 | 89.1 | 67.0 | 47.4 | 4,821,843 | 208,838 | 136,335 | 24.3 | 4.33 | 0.0 | 0.99 | |
| HapCut2 | 9.1 | 55.9 | 84.5 | 55.6 | 52.9 | 493,723 | 279,218 | 367,400 | 31.5 | 6.33 | 8.9 | 1.53 | |
| WhatsHap | 9.2 | 56.9 | 84.4 | 55.3 | 53.0 | 493,723 | 279,218 | 324,450 | 31.5 | 5.47 | 8.9 | 1.51 | |
| NA19240 (Chr6) (ONT 26x) | phasebook | 380.8 | 84.4 | 87.5 | 53.9 | 55.1 | 90,219 | 85,595 | 51,291 | 20.6 | 36.96 | 0.0 | 1.87 |
| phasebook-hi | 335.5 | 79.4 | 83.7 | 46.3 | 45.9 | 127,968 | 122,097 | 63,798 | 22.3 | 40.12 | 0.0 | 1.76 | |
| Canu | 169.2 | 65.4 | 83.9 | 40.7 | 40.8 | – | – | 129,586 | 22.5 | 35.40 | 0.0 | 0.98 | |
| Falcon | 179.3 | 64.0 | 77.7 | 33.7 | 35.4 | 69,660 | 37,993 | 162,461 | 20.5 | 35.72 | 0.0 | 1.02 | |
| Flye | 167.4 | 57.3 | 89.4 | 40.1 | 48.3 | – | – | 115,043 | 25.1 | 31.85 | 0.0 | 0.99 | |
| Shasta | 164.9 | 62.7 | 76.8 | 33.2 | 34.2 | – | – | 190,758 | 20.2 | 39.98 | 0.0 | 0.99 | |
| Wtdbg2 | 166.7 | 60.6 | 78.3 | 33.2 | 33.9 | – | – | 160,729 | 20.4 | 35.13 | 0.0 | 0.98 | |
| HapCut2 | 341.3 | 56.2 | 96.3 | 71.2 | 71.2 | 27,552,232 | 3,285,944 | 105,889 | 23.0 | 29.39 | 0.4 | 1.68 | |
| WhatsHap | 341.3 | 56.4 | 96.2 | 71.1 | 71.3 | 27,552,232 | 3,520,811 | 102,096 | 23.0 | 28.45 | 0.4 | 1.70 | |
| HG002 (ONT 38x) | phasebook | 5691 | – | 92.0 | 62.2 | 63.2 | 390,659 | – | 202,723 | 26.6 | 2.28 | 0.0 | – |
| Canu | 2901 | – | 84.5 | 39.3 | 51.6 | – | – | 266,624 | 23.2 | 10.27 | 0.0 | – | |
| Flye | 2928 | – | 83.9 | 38.5 | 50.6 | – | – | 287,619 | 23.0 | 11.94 | 0.0 | – | |
| Shasta | 2805 | – | 88.8 | 40.9 | 53.2 | – | – | 276,802 | 25.0 | 12.59 | 0.0 | – | |
| Wtdbg2 | 2794 | – | 83.0 | 34.4 | 44.2 | – | – | 239,707 | 22.8 | 9.62 | 0.0 | – | |
The publicly released assemblies of HG002 (Canu, Flye, Shasta, Wtdbg2) were directly used for comparison. We failed to run HapCut2 and WhatsHap for HG002 data on a computing machine (48 cores, 1 TB RAM) probably due to running out of memory