Table 1.

Assembly statistics.

Genotype	Kingdom	Haploid size	Chromosomes	Technology	Markers (per Mb)	Input sequences		Results a
									HaploSplit	HaploFill
C. albicans	Fungi	14 Mb	7 + R	PacBiob	116 (8.3)c	Primary	15.5 Mb	Hap 1	11.6 Mb	12.9 Mb
						Haplotigs	13.8 Mb	Hap 2	12.4 Mb	13.7 Mb
						Total	29.2 Mb	Unpl	5.2 Mb	2.7 Mb
A. thaliana	Plantae	119 Mb	5	PacBiod	676 (5.7)e	Primary	140.0 Mb	Hap 1	109.0 Mb	114.7 Mb
						Haplotigs	104.9 Mb	Hap 2	106.6 Mb	111.5 Mb
						Total	245.0 Mb	Unpl	29.4 Mb	19.0 Mb
B. taurus	Animalia	2.6 Gb (29+X) 2.5 Gb (29 + Y)	29 + XY	PacBiof	46,325 (17.6)g	Primary	2.7 Gb	Hap 1	2.6 Gb (29+X)	2.6 Gb (29+X)
						Haplotigs	2.5 Gb	Hap 2	2.3 Gb (29+Y)	2.5 Gb (29+Y)
						Total	5.2 Gb	Unpl	0.3 Gb	0.2 Gb
V. vinifera cv. Cabernet Franc	Plantae	487–557 Mbh	19	PacBio + Doveatil HiCi	1,661 (3.5)j	Primary	570.2 Mb	Hap 1	350.8 Mb	455.6 Mb
						Haplotigs	284.7 Mb	Hap 2	263.4 Mb	410.9 Mb
						Total	854.9 Mb	Unpl	239.9 Mb	47.1 Mb
M. rotundifolia	Plantae	483 Mb	20	PacBio + BioNanok	1,661 (3.5)l	Primary	459.5 Mbm	Hap 1	374.3 Mb	400.5 Mb
						Haplotigs	364.8 Mbn	Hap 2	338.9 Mb	370.0 Mb
						Total	896.0 Mb	Unpl	165.5 Mb	63.0 Mb

Summary statistics for the testing dataset.

^aWhere Hap 1: Haplotype 1; Hap 2: Haplotype 2; Unpl: Unplaced sequences.

^bFalconUnzip (Hamlin et al. 2019).

^c Forche et al. (2004).

^dFalconUnzip (Chin et al. 2016).

^e Singer et al. (2006).

^fFalconUnzip (Koren et al. 2018).

^g Low et al. (2020) using the Integrated Bovine Map of sex chromosome (ver. Btau_4.0, https://www.hgsc.bcm.edu/other-mammals/bovine-genome-project).

^hRange of values as reported for PN40024 in Jaillon et al. (2007) and Cabernet Sauvignon in Cochetel et al. (2021).

ⁱFalconUnzip + SSPACE + HiRise (Vondras et al. 2021).

^j Zou et al. (2020).

^kFalconUnzip + Hybrid Scaffolder (Cochetel et al. 2021).

^l Zou et al. (2020).

^mReported for FalconUnzip assembly as haplotype separation is lost during Hybrid Scaffolding.

ⁿReported for FalconUnzip assembly as haplotype separation is lost during Hybrid Scaffolding.