https://github.com/sebastian-gregoricchio/snhic

Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.
https://github.com/sebastian-gregoricchio/snhic

compartments dchic genova hi-c hic hicexplorer loop selfish snakemake snakemake-pipeline stripenn tad

Last synced: 15 days ago
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Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.

• Host: GitHub
• URL: https://github.com/sebastian-gregoricchio/snhic
• Owner: sebastian-gregoricchio
• License: gpl-3.0
• Created: 2022-04-01T10:53:30.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2025-03-05T08:38:21.000Z (over 1 year ago)
• Last Synced: 2026-04-04T02:29:28.721Z (2 months ago)
• Topics: compartments, dchic, genova, hi-c, hic, hicexplorer, loop, selfish, snakemake, snakemake-pipeline, stripenn, tad
• Language: Python
• Homepage: https://sebastian-gregoricchio.github.io/snHiC/
• Size: 5.73 MB
• Stars: 5
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md
  • License: LICENSE
  • Citation: citation.cff

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README

          
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# snHiC [](https://sebastian-gregoricchio.github.io/snHiC)

## 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](https://www.nature.com/articles/s41467-022-34626-6)) 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











## Documentation [](https://github.com/sebastian-gregoricchio/snHiC/wiki)

Details on the [installation](https://github.com/sebastian-gregoricchio/snHiC/wiki/2.-Installation-and-dependencies) and [usage](https://github.com/sebastian-gregoricchio/snHiC/wiki/3.-Run-the-pipeline) of snHiC can be found at the dedicated [Wiki](https://github.com/sebastian-gregoricchio/snHiC/wiki/).





-----------------

## Package history and releases

A list of all releases and respective description of changes applied could be found [here](https://sebastian-gregoricchio.github.io/snHiC/NEWS).

## Contact

For any suggestion, bug fixing, commentary please report it in the [issues](https://github.com/sebastian-gregoricchio/snHiC/issues)/[request](https://github.com/sebastian-gregoricchio/snHiC/pulls) tab of this repository.

## License

This repository is under a [GNU General Public License (version 3)](https://sebastian-gregoricchio.github.io/snHiC/LICENSE.md/LICENSE).




#### Contributors

[![contributors](https://contrib.rocks/image?repo=sebastian-gregoricchio/snHiC)](https://sebastian-gregoricchio.github.io/)