Software Open Access
Lazaris, Charalampos; Kelly, Stephen; Tsirigos, Aristotelis
HiC-bench: a Hi-C analysis pipeline that allows combinatorial parameter exploration and benchmarking
HiC-bench is a configurable computational pipeline that allows comprehensive and reproducible analysis of Hi-C sequencing data. It has the following characteristics:
It performs complete Hi-C analysis starting with the alignment of reads (fastq files) and ending with the annotation of specific interactions, their visualization and enrichment analysis.
It is the first Hi-C pipeline that integrates TAD calling using published methods and our own algorithm.
It performs calculation of boundary scores using our own methods and existing ones.
Every pipeline step is followed by summary statistics (when applicable) and visualization of the results. This allows quality control and facilitates troubleshooting.
It is fully expandable and customizable. Users can follow the included wrapper script template in order to add new tools.
It allows parameter exploration and comparison of different methods in a combinatorial fashion. This unique feature facilitates the design and execution of complex benchmark studies that may involve combinations of multiple parameter/tool choices in each step
It has been built with reproducibility in mind. All parameter settings are automatically logged.