Additional file 2: Table S1. of HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking

HiC-bench task implementation. The table summarizes how the pipeline tasks are implemented, which are the requirements for their execution and how they are handled by the pipeline-master-explorer script. The first column lists all the tasks performed by the pipeline ranging from alignment to annotation. The second column lists the input directory required for each task while the third one lists the parameter files. Certain tasks depend on the reference genome (human or mouse), thus the genome assembly acts as split variable (column 4). In some tasks, replicates can be grouped using the group variable (column 5). Pairwise comparisons between replicates or samples are also allowed using tuples (column 6). The last column lists the full pipeline-master-explorer command for each pipeline task. (XLSX 10 kb)