Skip to main content

Table 1 Feature comparison of different Hi-C analysis tools. Tools included in the comparison are Cooler [38]/HiGlass [39], Juicer [37]/Juicebox [40], HOMER [41], HiC-Pro [42], HiC-bench [43], TADbit [44], HiFive [45], HicDat [46], HiCInspector [47], HiCUP, HiCExplorer [48, 49], and HiCeekR [50]. 1: Only for interactive plotting; 2: Support for Juicer and Cooler multi-resolution files, but no native support; 3: Cooler ecosystem includes pairtools, cooler, cooltools, HiGlass, and distiller; 4: In conjunction with Juicebox; 5: Provides instructions for mapping, but no dedicated command; 6: Visualisation through Treeview; 7: With export for Fit-Hi-C; 8: Through compatibility with HiCPlotter; 9: Via HiCNorm; 10: Fit-Hi-C, C-loops, and targeted virtual 5C (in-house); 11: Only pre-processing; 12: For interactive visualisation; 13: SAM/BAM visualisation through SeqMonk; 14: via pyGenomeTracks; 15: Only when previously marked in BAM file; 16: via spacewalk; 17: no dedicated function, but possible via API; 18: Via Galaxy; 19: Includes hierarchical clustering of TADs; 20: Personal communication by developers, not currently documented; 21: insulation and compartment scores; 22: via TADkit

From: FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data

 

FAN-C

Cooler3

Juicer

HOMER

HiC-Pro

HiC-bench

TADbit

HiFive

HicDat

HiC-inspector

HiCUP

HiCExplorer

HiCeekR

User interfaces

 Command line

x

x

x

x

x

x

x

x

 

x

x

x

 

 Programmatic access (API)

x

x

x

   

x

x

x

    

 Graphical user interface (GUI)

1

1

4

   

1

 

11

12

 

18

x

Supported formats

 Directly compatible

 Juicer

x

 

x

  

20

       

 Cooler

x

x

   

20

     

x

 

 Custom/Native

x

x

x

x

x

x

x

x

x

x

x

x

x

 Import

 Juicer

x

x

  

x

      

x

 

 Cooler

x

x

  

x

 

x

    

x

 

 TXT file

x

x

 

x

x

x

x

x

 

x

 

x

 

 FASTQ

x

x

x

5

x

x

x

 

5

x

x

x

 

 SAM/BAM

x

x

x

x

x

x

x

x

x

  

x

 

 hiclib

 

x

           

 Export

 Juicer

x

 

x

x

x

20

    

x

  

 Cooler

x

x

  

x

20

x

    

x

 

 GInteractions

           

x

 

 TXT file

x

x

x

x

x

x

x

  

x

x

x

x

Matrix generation

 FASTQ mapping

 Simple mapping

x

x

 

5

x

x

x

 

5

x

x

5

 

 Iterative mapping

x

     

x

      

 Ligation junction split

x

 

x

x

x

 

x

   

x

  

 Read/region pair filtering

 Mapping Quality

x

x

x

 

x

x

    

x

x

 

 Multi-mapping reads

x

x

x

 

x

x

x

   

x

x

 

 Restriction site distance

x

x

x

x

 

x

x

x

 

x

x

x

x

 Ligation errors

x

x

x

 

x

 

x

x

x

 

x

x

x

 Self-ligations

x

x

x

x

x

x

x

x

x

 

x

x

x

 PCR duplicates

x

x

x

x

x

x

x

x

  

x

x

15

 Unusual read density

 

x

 

x

  

x

      

 Quality statistics

x

x

x

x

x

x

x

x

 

x

x

x

 

 Hi-C processing

 Fragment-level Hi-C

x

x

x

x

x

x

 

x

x

  

x

 

 Equi-distant bins

x

x

x

x

x

x

x

x

x

x

 

x

x

 Multi-resolution Hi-C

2

x

x

  

20

 

x

   

x

 

 Matrix balancing

x

x

x

x

x

x

x

x

x

  

x

x

 Probabilistic normalisation

       

x

x

    

 Matrix merge

x

x

x

  

x

x

 

x

  

x

 

 Allele-specific matrices

 

x

x

 

x

        

 Mixed restriction cut sites

x

x

x

 

x

      

x

 

 Hi-C filtering

 Minimum coverage

x

x

  

x

 

x

x

     

 Diagonal

x

x

  

x

x

       

Matrix analysis

 Comparisons

 PCA (sample comparison)

x

17

   

21

       

 Matrix fold-change

x

x

x

  

20

  

x

  

x

 

 Matrix difference

x

17

x

  

20

     

x

 

 Score/feature comparisons

x

17

x

x

 

x

x

    

x

 

 Correlations

 

17

x

x

 

x

x

 

x

  

x

 

 Domains

 Insulation score

x

x

   

x

x

    

x

 

 Directionality index

x

x

   

x

      

x

 Arrowhead

  

x

          

 TAD calling

  

x

x

 

x

x

    

19

x

 Loops

 HICCUPS

x

x

x

          

 Other

   

x

7

10

     

x

 

 Common Hi-C analyses

 Expected values

x

x

x

x

 

x

x

x

x

x

 

x

 

 AB compartments

x

x

x

x

 

20

x

 

x

  

x

x

 Aggregate Hi-C matrices

x

x

x

        

x

 

 3D modelling

  

16

   

x

      

 Other

 Compaction

   

x

         

Visualisation

 Hi-C matrix

x

x

x

6

8

8

22

x

x

x

13

x

x

 Triangular Hi-C matrix

x

x

 

6

8

8

22

x

   

x

 

 Other genomic tracks

x

x

x

 

8

8

22

    

14

x

 Genes

x

x

x

 

8

8

22

      

 Virtual 4C

x

x

x

  

8

      Â