This pipeline is based on the HiC-Pro workflow. It was designed to process Hi-C data from raw fastq files (paired-end Illumina data) to normalized contact maps. The current version supports most protocols, including digestion protocols as well as protocols that do not require restriction enzymes such as DNase Hi-C. In practice, this workflow was successfully applied to many data-sets including dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChip data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Pipeline summary

  1. Mapping using a two steps strategy to rescue reads spanning the ligation sites (bowtie2)
  2. Detection of valid interaction products
  3. Duplicates removal
  4. Create genome-wide contact maps at various resolution
  5. Contact maps normalization using the ICE algorithm (iced)
  6. Quality controls and report (MultiQC)
  7. Addition export for visualisation and downstream analysis (cooler)

Quick Start

i. Install nextflow

ii. Install one of docker, singularity or conda

iii. Download the pipeline and test it on a minimal dataset with a single command

nextflow run hic -profile test,<docker/singularity/conda>

iv. Start running your own analysis!

nextflow run hic -profile <docker/singularity/conda> --reads '*_R{1,2}.fastq.gz' --genome GRCh37

See usage docs for all of the available options when running the pipeline.


The nf-core/hic pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don’t hesitate to get in touch on Slack. You can join with this invite.


nf-core/hic was originally written by Nicolas Servant.


If you use nf-core/hic for your analysis, please cite it using the following doi: 10.5281/zenodo.2669513

You can cite the nf-core pre-print as follows: Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.