Table 1 Analysis tools for Hi-C data

Distiller [163]

Matrix generation

Python package/Linux command line

.fastq

.mcool and .cool

HiCExplorer [214]

Matrix generation

Linux command line

.sam, .bed

.cool or .mcool

Hiclib [162]

Matrix generation

Linux command line

.fastq

.hdf5

HiC-Pro [160]

Matrix generation

Linux command line

.bed

.matrix

HiCUP [215]

Matrix generation

Linux command line

.fastq

.bam

HOMER [36]

Matrix generation

Linux command line/Mac/Windows

.fastq

.txt with matrix information, or .hic

Juicer [161]

Matrix generation

Linux command line

.fastq

.hic

TADbit [216]

Matrix generation

Python package/Linux command line

.fastq, .dsrc

.map

Arrowhead [141]

TAD calling

Linux command line

.hic

.bedpe

CaTCH [176]

TAD calling

R package

.hic

A list of data frame with domain information in R

Domaincaller (Directionaliy Index) [169]

TAD calling

Linux command line

.cool

.bed and .bedgraph

HiCDB [217]

TAD calling

R package/Linux command line with MATLAB

N x N matrix, or K × 3

.txt

HiCseg [175]

TAD calling

R package

Data in r matrix format

List of t_hat, J, and t_est_mat data in R

HOMER [36]

TAD calling

Linux command line/Mac/Windows

HiC tag directory from HOMER

.2D.bed

TADbit [216]

TAD calling

Python package/Linux command line

.bam or .map

List of TADs in Python

TADCompare [218]

TAD calling

R package

N x N matrix, x (N + 3) matrix, or 3-column matrix

Data frame in R

TADPole [219]

TAD calling

R package

Tab-separated matrix file

TADpole object in R

TADtree [220]

TAD calling

Linux command line through Python script

Contact matrix without column or row labels

.txt files with three columns for contact domain information

TopDom [174]

TAD calling

R package

Tab-separated matrix file with bin information

.binsignal and.domain

3DNetMod [221]

TAD calling

Linux command line through Python script

.bed and tab-separated matrix file

Genomic coordinates and statistics output files 

FitHiC [179]

Loop calling

R pacakge/Linux command line with Python script

Fragment file and interaction file

.txt

FitHiC2 [180]

Loop calling

Linux command line

Fragment file and matrix file

.txt

GOTHiC [178]

Loop calling

R package

.bam or bowtie2 alignment output

Data frame in R

HiCCUPS [141]

Loop calling

Linux command line

.hic

.bedpe

HiC-DC [222]

Loop calling

Linux command line through R script

File with Hi-C covariates and Hi-C counts

File with data.table and fit information

HiCNormCis (FIREcaller) [223]

Loop calling

R package

N x N matrices file

Object in R

HOMER [36]

Loop calling

Linux command line/Mac/Windows

HiC tag directory from HOMER

.2D.bed

Mustache [182]

Loop calling

Linux command line

.hic, .cool, or raw contact map with normalization vector .txt file and bias .txt file

.tsv file with contact domain information and mustache scale

SIP [181]

Loop calling

Linux command line

.hic, .mcool, or processed file with normalized value

Loop file that can be loaded into Juicebox

StripeCaller [224]

Loop calling

Linux command line

.cool

.bedpe

HiCRep [184]

Reproducibility testing

R package

Squared matrix, 3-column matrix, .hic or .cool

Object in R

HiC-Spector [185]

Reproducibility testing

Linux command line for both Julia and Python implementation

.hic or text delimited matrix file

Reproducibility score

IDR2D [183]

Reproducibility testing

Linux command line

.hic or .matrix and.bed from HiC-Pro

IDR and significance value

FIND [187]

Differential analysis

R package

Three column tab-separated file with matrix and four-column tab-separated file, or .hic

Object in R

HiCCompare [186]

Differential analysis

R package

.hic, .cool, or .matrix, and .bed from HiC-Pro

Object in R

Selfish [188]

Differential analysis

Linux command line

.hic, .cool, .bed, or .matrix

Matrix of q-values in binary numpy file