snHiC is a snakemake based end-to-end pipeline to analyze Hi-C data. The input files required to run the pipeline are Paired-End fastq files. The pipeline performs data quality control, normalization and correction. It also includes the possibility to perform grouped analyses (e.g, merging of replicates) besides TAD, loops and stripes detection and differential contacts and compartment analyses. Notabily, the latter is performed using dcHiC, a recently published method (A. Chakraborty, et al., Nat. Comm. 2022) that enables more precise and high-resolution differential compartment analyses.

If you use this pipeline, please cite:

Details on the installation and usage of snHiC can be found at the dedicated Wiki.

A list of all releases and respective description of changes applied could be found here.

For any suggestion, bug fixing, commentary please report it in the issues/request tab of this repository.

This repository is under a GNU General Public License (version 3).