Table 1.
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 |
aHiclib keeps the reads with only one mapped end (single-sided reads) for use in coverage computations
bHIPPIE states that it rescues chimeric reads. No details are given
cHiCdat reports no substantial improvement in successfully aligned read pairs when iterative mapping in Hiclib is used for Arabidopsis thaliana Hi-C data
dHiCdat provides three options for normalization: coverage and distance correction, HiCNorm and ICE
eHOMER provides two options for normalization: simpleNorm corrects for sequencing coverage only and norm corrects for coverage plus the genomic distance between loci
fHiTC provides two options for normalization: normLGF implements HiCNorm and normICE implements ICE algorithm from Hiclib
gHiFive provides three options - Probability, Express, and Binning - for normalization. The Express and Binning algorithms correspond to matrix balancing and explicit-factor correction schemes, respectively