: a complete and simplified snakemake pipeline for grouped Hi-C data analysis.

SUMMARY

Genome-wide chromosome conformation capture (Hi-C) is a technique that allows the study of 3D genome organization. Despite being widely used, analysis of Hi-C data is technically challenging and involves several time-consuming steps that often require manual involvement making it error prone, potentially affecting data reproducibility. In order to facilitate and simplify these analyses we implemented , a snakemake-based pipeline that allows for the generation of contact matrices at multiple resolutions in one single run, aggregation of individual samples into user-specified groups, detection of domains, compartments, loops and stripes and performance of differential compartment and chromatin interaction analyses.

AVAILABILITY AND IMPLEMENTATION

Source code is freely available at https://github.com/sebastian-gregoricchio/snHiC. A yaml-formatted file (snHiC/workflow/envs/snHiC_conda_env_stable.yaml) is available to build a compatible conda environment.

SUPPLEMENTARY INFORMATION

Supplementary data are available at online.