1. Introduction

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.

Citation

If you use this pipeline, please cite:

S. Gregoricchio & W. Zwart. "snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis".
Bioinformatics Adavances, Volume 3, Issue 1, 2023, vbad080
DOI: 10.1093/bioadv/vbad080