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

Table 1 Benchmarking results for Caenorhabditis elegans data

Assembler	Size (bp)	Max Length (bp)	N50 (bp)	#misassembly	#switch error
Platanus-allee + GreenHill	208,814,372	20,808,020	17,065,040	105	1,657
FALCON-Unzip + GreenHill	204,407,441	20,723,971	17,142,644	108	2,121
FALCON-Unzip + 3D-DNA	226,102,670	22,381,602	16,567,875	286	2,444
FALCON-Unzip + SALSA2	216,393,292	13,113,712	9,455,592	104	2,244
Canu + GreenHill	195,748,221	19,835,919	16,219,706	182	1,742
Canu + 3D-DNA	223,116,127	21,318,404	14,712,650	665	2,165
Canu + SALSA2	209,942,443	15,218,531	6,564,248	315	1,989

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