TABLE 2.

Comparison of computational programs for proximity‐based genome scaffolding. The programs are sorted in the descending order of the number of citations in the literature introducing the individual programs, with the exception of the programs that are not openly maintained (LACHESIS and HiRise at the bottom)

Program	Description	Input data requirement	Other information
3d‐dnaa,b	Misjoin correction algorithm is applied to detect errors in the input assembly; compatible with multiple enzymes	Accepts only Juicer mapper format	The results can be reviewed and modified directly by JuiceBox
SALSA2c	Uses the physical coverage of Hi‐C pairs to identify misassembled regions of the input assembly; compatible with multiple enzymes	Generic bam (bed) file, assembly graph, unitig, 10x link files	The results can be visualized by JuiceBox via the included script
ALLHiCd	Scaffolding and phasing of a polyploid genome	Hi‐C read pairs; (option) associated gene annotation or chromosome‐scale genome assembly for a closely related species	Generate the chromatin contact matrix to evaluate genome scaffolding
FALCON‐Phasee	Scaffolding and phasing of a diploid genome	Hi‐C read pairs; FALCON‐Unzip assembly	Output two phased full‐length pseudo‐haplotypes
HiCAssemblerf	Misassemblies are corrected by iterative joining of high‐confidence scaffold paths	Hi‐C matrix of h5 format created by HiCExplorer	Misassembled regions in the input assembly can be corrected by specifying the location in the program
instaGRAALg	Overhauling the GRAAL program to allow efficient assembly of large genomes	Hi‐C matrix of instaGRAAL format created by hicstuff or HiC‐Box	Requires NVIDIA CUDA and can be executed in a limited environment
LACHESISh	No function to correct scaffold misjoins	Generic bam format	Developer's support discontinued; intricate installation
HiRisei	Employed in Dovetail Chicago/Hi‐C service	Generic bam format	Open‐source version at GitHub not updated since 2015

^aDudchenko et al., 2017; ^bDurand et al., 2016; ^cGhurye et al., 2019; ^dZhang et al., 2019; ^eKronenberg et al., 2018; ^fRenschler et al., 2019; ^gBaudry et al., 2020; ^hBurton et al., 2013; ⁱPutnam et al., 2016.