Table 1.
Assembly statistics. HiFi read N50: 50% of HiFi reads are longer than this number. Contig NG50: minimum contig length needed to cover 50% of the known genome (GRCh38). Contig NGA50: similar to NG50, but based on contig alignment lengths to GRCh38 instead of contig sizes. Phasing switch error rate: percent adjacent SNP pairs are wrongly phased. Phasing hamming error rate: percent SNPs wrongly phased in comparison to true phases.
| Sample | HG002 (NA24385) | NA12878 | PGP1 | HG00733 | ||||
|---|---|---|---|---|---|---|---|---|
| Long-read coverage | 29.7 (HiFi) | 30.1 (HiFi) | 23.9 (HiFi) | 33.4 (HiFi) | 93.0 (CLR) | |||
| Long read N50 (bp) | 13,480 | 10,004 | 12,974 | 11,769 | 33,090 | |||
| Hi-C read coverage | 38.5 | 44.8 | 261.7 | 35.5 | 67.1 | |||
| Assembly algorithm | Trio Canu | Trio Peregrine | DipAsm | DipAsm | DipAsm | DipAsm | Strand-seq | Falcon-Phase |
| Scaffolding | 3D-DNA | HiRise | HiRise | 3D-DNA | ||||
| Paternal / maternal contig size (Gbp) | 2.96 / 3.04 | 2.81 / 2.88 | 2.98 / 2.97 | 2.97 / 2.97 | 2.98 / 2.98 | 2.93 / 2.93 | 2.90 / 2.90 | 2.89 / 2.89 |
| Paternal / maternal contig NG50 (Mbp) | 15.5 / 18.3 | 16.6 / 15.2 | 25.2 / 24.3 | 19.6 / 18.7 | 15.1 / 18.4 | 25.2 / 26.2 | 28.5 / 23.6 | 22.3 / 22.3 |
| Paternal / maternal contig NGA50 (Mbp) | 10.2 / 12.8 | 11.0 / 10.6 | 14.3 / 13.5 | 12.7 / 12.1 | 10.3 / 11.0 | 16.0 / 16.6 | 15.8 / 15.8 | 14.3 / 13.7 |
| Phasing switch / hamming error rate (%) | 0.38 / 0.23 | 0.38 / 0.31 | 0.50 / 0.49 | 0.15 / 2.13 | 0.21 / 1.63 | 0.16 / 0.60 | 0.30 / 0.70 | 0.43 / 35.8 |
| SNP / INDEL false positive rate (×10⁻⁶) | 1.9 / 31.6 | 2.6 / 32.0 | 2.4 / 27.7 | 2.0 / 4.2 | ||||
| SNP / INDEL false negative rate (%) | 4.31 / 5.85 | 3.28 / 5.00 | 0.36 / 2.09 | 0.56 / 1.22 | 3.32 / - | 4.00 / - | 7.89 / - | |
| SV sensitivity / precision (%) | 90.7 / 92.8 | 90.6 / 92.6 | 93.4 / 92.6 | |||||