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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