Table 1.

Validation of CHM13 assemblies.

Asm	NG50 (Mb)	#Errors Quast / VerityMap	%Comp	Mismatch /100 kb	Indel /100 kb	Resolved BACs	T2T	>95%
Verkko	135.13	21 / 20	99.75	2.46	0.61	644 / 644	12	17
Verkko (HiFi)	70.13	17 / 20	99.42	2.17	0.55	629 / 644	1	3
LJA	96.69	12 / 29	99.60	2.14	0.85	639 / 644	6	9
Flye	69.53	114 / 30	93.58	6.03	110.92	511 / 644	0	0
Hifiasm	90.22	32 / 39	99.54	2.55	0.70	643 / 644	2	5

We used the published reference of CHM13v1.1 ¹⁴ to evaluate the assemblies with QUAST and ran VerityMap as a reference-free alternative. The relative assembler ranking between QUAST and VerityMap shows good agreement, only switching LJA and Verkko in terms of fewest errors. %Comp: chromosome completeness as measured by QUAST alignments. Number of mismatches and Indels reported by QUAST are given per 100 kb. T2T: reports complete chromosomes with a single unitig covering >99% of the reference bases and having canonical telomeres on each end. >95%: reports chromosomes with a single unitig covering >95% of the reference with no requirement for telomeres. QUAST errors intersecting known heterozygous variants or errors ³⁷, as well as those within the core rDNA arrays, were excluded using a filter script from Shafin et al. ⁴. CHM13 reference BACs were evaluated as in Nurk et al. ⁸. Canonical telomeres were identified using the VGP pipeline ¹⁰. The best result for each coverage level and category is highlighted in bold.