Table 1.
A comparison of dataset and scaffold accuracy metrics before and after running HiC-Hiker
| Species | Human (NA12878) | Worm (VC2010) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Assembler | w2rap + Illumina | Canu + ONT | SPAdes + Illumina | |||||||||
| Contig N50 (kb) | 68.6 | 4821.0 | 41.0 | |||||||||
| Contig maximum length (kb) | 934.6 | 34 607.7 | 283.5 | |||||||||
| Scaffolding software | 3D-DNA | SALSA2 | 3D-DNA | ALLHiC | SALSA2 | |||||||
| W/o graph | W/ graph | |||||||||||
| Minimum length threshold | 15k | — | — | 15k | 5k | 50k | 15k | 15k | 15k | |||
| Hi-C coverage | 7× | 7× | 7× | 7× | 7× | 14× | 28× | 7× | 7× | |||
| Threshold K | 75 kb | 75 kb | 75 kb | 7.5 kb | 75 kb | 200 kb | 75 kb | 75 kb | 75 kb | 75 kb | ||
| Raw scaffolds >1 Mb before (after) manual correction | ||||||||||||
| No. of scaffolds | 95 (23) | 75 | 81 | 6 | 7 | 6 | 6 | 6 | 6 | 5 | ||
| Total bases (Mb) | 2391.4 (2392.0) | 2624.8 | 2622.8 | 77.5 | 89.8 | 39.4 | 77.9 | 78.0 | 77.8 | 7.4 | ||
| Maximum length (Mb) | 127.7 (205.1) | 273.4 | 188.9 | 16.0 | 18.7 | 8.8 | 16.1 | 16.2 | 16.2 | 1.8 | ||
| Anchoring | 99.75% (99.74%) | 90.42% | 96.76% | 99.03% | 95.89% | 95.31% | 98.89% | 98.61% | 98.24% | — | ||
| Ordering | 98.39% (89.62%) | 90.95% | 93.20% | 99.79% | 99.37% | 99.62% | 99.82% | 99.81% | 98.93% | — | ||
| Local ordering | 90.58% (89.97%) | 90.24% | 92.41% | 85.71% | 84.71% | 84.25% | 89.04% | 91.20% | 91.57% | — | ||
| Orientation | 91.57% (90.95%) | 90.31% | 92.48% | 86.31% | 85.37% | 84.82% | 89.72% | 91.95% | 92.46% | — | ||
| Local orientation | 95.72% (95.70%) | 96.00% | 96.34% | 88.35% | 86.07% | 87.24% | 89.83% | 92.04% | 93.01% | — | ||
| HiC-Hiker output | ||||||||||||
| Anchoring | 99.74% | 90.44% | 96.75% | 99.03% | 99.00% | 99.01% | 95.17% | 95.32% | 98.90% | 98.63% | 98.23% | — |
| Ordering | 89.64% | 88.42% | 94.74% | 99.76% | 99.80% | 99.81% | 99.26% | 99.64% | 99.82% | 99.84% | 98.98% | — |
| Local ordering | 91.09% | 90.42% | 92.28% | 81.06% | 88.89% | 89.11% | 85.57% | 84.65% | 92.43% | 93.93% | 92.28% | — |
| Orientation | 92.19% | 90.49% | 92.36% | 81.51% | 89.61% | 89.85% | 86.58% | 85.20% | 93.28% | 94.78% | 93.06% | — |
| Local orientation | 98.25% | 96.67% | 96.73% | 84.45% | 93.75% | 93.69% | 92.06% | 88.78% | 95.83% | 96.68% | 93.80% | — |
| No. of contig flip | ||||||||||||
| True positives | 1139 | 33 | 39 | 119 | 118 | 115 | 207 | 31 | 125 | 96 | 38 | — |
| True negatives | 35 157 | 1124 | 1122 | 1179 | 1323 | 1325 | 1962 | 317 | 1439 | 1507 | 1505 | — |
| False positives | 193 | 30 | 31 | 179 | 35 | 33 | 66 | 25 | 27 | 19 | 25 | — |
| False negatives | 453 | 34 | 30 | 60 | 61 | 64 | 122 | 19 | 41 | 36 | 77 | — |