GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C

Table 5 Benchmarking results for other species

Species	Assembler	Input for contigs	Size (bp)	Max Length (bp)	N50 (bp)	QV	Switch error rate	Phasing accuracy
Budgerigar	FALCON-Unzip + GreenHill	CLR	2,273,118,342	140,405,933	88,135,996	40.78	0.28	0.896
	FALCON-Unzip + 3D-DNA		2,620,388,952	159,155,647	90,074,506	39.20	0.36	0.701
	FALCON-Unzip + SALSA2		2,437,415,698	95,254,517	34,574,245	39.31	0.34	0.741
Black rhinoceros	Hifiasm + GreenHill	HiFi	5,325,705,542	101,752,101	52,259,952	58.44	0.05	0.982
	Hifiasm + 3D-DNA		6,523,963,142	136,733,613	48,162,421	55.16	0.09	0.615
	Hifiasm + SALSA2		6,206,904,826	40,586,421	3,069,332	55.53	0.05	0.785
	Hifiasm Hi-C mode		6,047,793,056	94,248,160	30,503,132	67.13	0.06	0.995
Sterlet	Hifiasm + GreenHill	HiFi	3,712,891,508	83,435,872	25,813,405	58.82	0.03	0.849
	Hifiasm + 3D-DNA		3,882,750,516	14,958,612	1,019,399	54.98	0.04	0.889
	Hifiasm + SALSA2		3,474,135,770	47,228,216	7,128,235	55.15	0.04	0.751
	Hifiasm Hi-C mode		3,748,196,843	55,271,118	9,593,284	60.99	0.02	0.975

Size and N50 were calculated for sequences whose length ≥ 500 bp. Size represents the size of assemblies generated by each assembler. QV and switch error rate were calculated by Merqury. Phasing accuracy represents the proportion of the majority of hap-mers in a scaffold, and a high value of this indicator suggests large-scale haplotype consistency. A bold value indicates the best one for each input assembly

ISSN: 1474-760X