Table 1 Software tools for Hi-C data analysis
From: Analysis methods for studying the 3D architecture of the genome
Tool | Short-read | Mapping | Read | Read-pair | Normalization | Visualization | Confidence | Implementation |
|---|---|---|---|---|---|---|---|---|
aligner(s) | improvement | filtering | filtering | estimation | language(s) | |||
HiCUP [46] | Bowtie/Bowtie2 | Pre-truncation | ✓ | ✓ | − | − | − | Perl, R |
Hiclib [47] | Bowtie2 | Iterative | ✓ a | ✓ | Matrix balancing | ✓ | − | Python |
HiC-inspector [131] | Bowtie | − | ✓ | ✓ | − | ✓ | − | Perl, R |
HIPPIE [132] | STAR | ✓ b | ✓ | ✓ | − | − | − | Python, Perl, R |
HiC-Box [133] | Bowtie2 | − | ✓ | ✓ | Matrix balancing | ✓ | − | Python |
HiCdat [122] | Subread | −c | ✓ | ✓ | Three options d | ✓ | − | C++, R |
HiC-Pro [134] | Bowtie2 | Trimming | ✓ | ✓ | Matrix balancing | − | − | Python, R |
TADbit [120] | GEM | Iterative | ✓ | ✓ | Matrix balancing | ✓ | − | Python |
HOMER [62] | − | − | ✓ | ✓ | Two options e | ✓ | ✓ | Perl, R, Java |
Hicpipe [54] | − | − | − | − | Explicit-factor | − | − | Perl, R, C++ |
HiBrowse [69] | − | − | − | − | − | ✓ | ✓ | Web-based |
Hi-Corrector [57] | − | − | − | − | Matrix balancing | − | − | ANSI C |
GOTHiC [135] | − | − | ✓ | ✓ | − | − | ✓ | R |
HiTC [121] | − | − | − | − | Two options f | ✓ | ✓ | R |
chromoR [59] | − | − | − | − | Variance stabilization | − | − | R |
HiFive [136] | − | − | ✓ | ✓ | Three options g | ✓ | − | Python |
Fit-Hi-C [20] | − | − | − | − | − | ✓ | ✓ | Python |