Table 1 Assembly statistics
From: Chromosome-scale, haplotype-resolved assembly of human genomes
Sample | HG002 (NA24385) | NA12878 | PGP1 | HG00733 | ||||
|---|---|---|---|---|---|---|---|---|
Assembly algorithm | Trio Canu | Trio Peregrine | DipAsm | DipAsm | DipAsm | DipAsm | Strand-seq | Falcon-Phase |
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 | |||
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 | – | – | – | – | – |
