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

Table 2 Benchmarking results for Drosophila melanogaster data

Assembly	Input for contigs	Size (bp)	Max Length (bp)	N50 (bp)	#misassembly	#switch error
Canu + GreenHill	CLR	298,393,407	32,550,496	25,267,681	515	2,316
Canu + 3D-DNA		377,404,855	14,057,924	637,829	1,095	2,604
Canu + SALSA2		318,193,525	23,535,552	12,777,832	661	2,409
HiCanu + GreenHill	HiFi	321,609,584	33,217,621	24,975,482	930	686
HiCanu + 3D-DNA		351,304,469	21,680,562	2,482,127	1,631	688
HiCanu + SALSA2		297,968,925	28,602,144	24,843,359	1,435	646
Hifiasm + GreenHill	HiFi	307,145,492	27,892,039	24,570,326	742	480
Hifiasm + 3D-DNA		371,012,458	33,126,928	1,795,858	2,546	752
Hifiasm + SALSA2		327,819,782	25,140,693	9,592,386	2,330	735
Hifiasm Hi-C mode		308,439,591	26,052,400	21,522,312	1,346	637

Size, N50, #misassembly, and #switch error were calculated for sequences whose length ≧500 bp. Size represents the size of assemblies generated by each assembler. #misassembly and #switch error is the number of misassemblies and switch errors calculated using the reference alignment-based method. A bold value indicates the best one for each input assembly

ISSN: 1474-760X