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Table 1 Comparison of HiC-bench with published Hi-C analysis or visualization tools

From: HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking

Hi-C tasks HiC-bench HiFive Hi-Cpipe HiCNorm hiclib HiTC HOMER Hi-Corrector HiC-Pro TADbit HiCUP HiC-Box HiCdat HIPPIE Sushi HiCPlotter
Alignment x   x   x     x x x x   x   
Filtering x x x   x     x x x x   x   
Genome browser tracks x                
Quality assessment plots x x x    x    x   x   x x   
Contact matrices x x x   x   x   x    x x    
Matrix correction x x   x x x x x x x   x x    
Matrix comparison x             x    
Boundary scores x                
Domains x          x       
Boundary comparison x                
Specific interactions x   x   x   x   x   x x x x   
Annotations x      x        x    
Allele-specific interactions          x   x      
Visualization x x x    x x       x   x x
Integration with ChIP-seq data x             x x   
Parallelization x x x     x x x x       
Integration of alternative tools x                
Parameter exploration x                
Reproducibility x x               
  1. HiC-bench is a comprehensive and feature-rich Hi-C analysis pipeline that performs various Hi-C tasks by combining our newly-developed tools with existing tools