Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references

Table 1 Summary of sequencing data from different platforms

Dataset	Sample	Platform	Data type	Reads	Total bases (bb)	Depth	Min Length	Max length	Average read length	N50	%GC
I002C	Child	PacBio	HiFi	8,986,857	152,977,790,522	50.99	8	63,921	17,022.40	17,132	40.78
		ONT	Duplex	6,561,950	193,663,321,924	64.55	1	191,644	29,513.10	38,128	40.85
		ONT	Ultralong	12,710,241	441,077,651,554	147.03	1	1,434,925	34,702.50	87,761	40.58
		MGI	Omni-C	1,476,892,046	222,216,283,752	74.07	150	150	150	150	42.5
I002A	Father	MGI	Short reads	717,979,504	107,696,925,600	35.9	150	150	150	150	40.48
I002B	Mother	MGI	Short reads	749,860,990	112,479,148,500	37.49	150	150	150	150	40.28
HG002	Child	Pacbio	HiFi	9,076,876	164,744,547,100	54.91	86	63,894	18,149.92	17,963	40.32
		ONT	Duplex	6,110,824	147,724,801,341	49.24	1	187,925	24,174.29	34,205	40.89
		ONT	Ultralong	1,347,597	204,361,988,910	68.12	100,000	2,486,048	151,649	147,890	40.54
		Illumina	Hi-C	596,026,484	89,999,999,084	30	151	151	151	151	42.09
HG003	Father	Illumina	Short reads	687,439,454	101,741,039,192	33.91	148	148	148	148	39.67
HG004	Mother	Illumina	Short reads	684,524,092	101,309,565,616	33.77	148	148	148	148	39.95

The coverage depth calculation was based on a genome size estimation of 3 Gb. PacBio Pacific Biosciences, HiFi High-Fidelity reads, ONT Oxford Nanopore Technologies

ISSN: 1474-760X