Table 1:

Overview of the specifications of major scaffolding programs

Program	Support and availability	Input data requirement	Other information	Literature
LACHESIS	Developer's support discontinued; intricate installation	Generic bam format	No function to correct scaffold misjoins	[4]
HiRise	Open source version at GitHub not updated since 2015	Generic bam format	Used in Dovetail Chicago/Hi-C service. Default input sequence length cut-off = 1,000 bp	[10]
3d-dna	Actively maintained and supported by the developer	Not compatible with multiple enzymes; accepts only Juicer mapper format	Default parameters: -t 15000 (input sequence length cut-off), -r 2 (No. of iterations for misjoin correction)	[13, 20]
SALSA2	Actively maintained and supported by the developer	Compatible with multiple enzymes; generic bam (bed) file, assembly graph, unitig, 10x link files	Default parameters: -c 1000 (input sequence length cut-off), -i 3 (No. of iterations for misjoin correction)	[11, 12]