HiC-bench: initial release (v0.1)

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.