Table 7 Loop caller algorithms overview (input, output, resolution)

1

FitHiC [29]

2014

Hi-C, ChIA-PET

.txt

.txt, .gz

2

HMRF Bayesian caller [36]

2015

Hi-C

.txt

\(\le 10\) KB

.hdf5, .txt

3

HiC-DC [33]

2017

Hi-C

.bam

\(\le 5\) KB

.rds

4

GOTHiC [32]

2017

Hi-C

.bam, .sam

\(\le 1Mb\)

.gz

5

cLoops [25]

2019

ChIA-PET, Hi-C, HiChIP, TrAC-looping

.bedpe

\(\le 5\) KB

.txt, .pdf

6

FitHiChIP [31]

2019

HiChIP, Hi-C

.txt, .gz, .sizes

\(\le 5\) KB

.bed

7

FitHiC2 [30]

2020

Hi-C

.txt

\(\le 40\) KB

.txt

8

FIREcaller [37]

2020

Hi-C

.gz, .hic, .cool

40 KB

.txt

9

Peakachu [38]

2020

Hi-C, Micro-C, ChIA-PET, HiChIP, PLAC-Seq, Capture Hi-C

.cool, .hic, .bedpe

10 KB

.bedpe

10

Coolpup.py [39]

2020

Hi-C

.bed, .cool, .mcool, .hic, .tsv

\(\le 10\) KB

.clpy

11

Mustache [40]

2020

Hi-C, Micro-C

.txt, .hic, .cool, .mcool

\(\le 10\) KB

.tsv

12

SIP & SIPMeta [41]

2020

Hi-C

.hic, .mcool, file

\(\le 5\) KB

file

13

Chromosight [42]

2020

Hi-C, ChIA-PET, DNA SPRITE, HiChIP, Micro-C

.cool

\(\le 10\) KB

.tsv

14

LASCA [24]

2021

Hi-C, ChIP-seq

.cool

\(\le 10\) KB

.bedpe

15

cLoops2 [26]

2021

ChIC-seq, Hi-TrAC/TrAC-looping

.bedpe

\(\le 1\) KB

.txt

16

HiC-ACT [28]

2021

Hi-C

.txt

\(\le 10\) KB

file

17

NeoLoopFinder [35]

2021

Hi-C

.mcool

10 KB

.bedGraph

18

LOOPbit [23]

2022

Hi-C

.tsv

5 KB

.tsv

19

HiCExplorer [27]

2022

Hi-C

.bam, .sam

\(\le 10\) KB

.h5

20

ZipHiC [34]

2022

Hi-C

.csv

\(\le 10\) KB

data frame

21

HiCCUPS [48]

2014

Hi-C

.hic

\(\le 5\) KB

text

22

DeepLoop [49]

2022

Hi-C

heatmap

\(\le 5\) KB

heatmap