# ![nf-core/hic](docs/images/nfcore-hic_logo.png)

**Analysis of Chromosome Conformation Capture data (Hi-C)**.

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
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![Singularity Container available](https://img.shields.io/badge/singularity-available-7E4C74.svg)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2669513.svg)](https://doi.org/10.5281/zenodo.2669513)

## Introduction

This pipeline is based on the
[HiC-Pro workflow](https://github.com/nservant/HiC-Pro).
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](https://www.nextflow.io), 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`](https://nf-co.re/usage/installation)

ii. Install one of [`docker`](https://docs.docker.com/engine/installation/),
[`singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or
[`conda`](https://conda.io/miniconda.html)

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

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

iv. Start running your own analysis!

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

See [usage docs](docs/usage.md) for all of the available options when running the pipeline.

## Documentation

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

1. [Installation](https://nf-co.re/usage/installation)
2. Pipeline configuration
    * [Local installation](https://nf-co.re/usage/local_installation)
    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
    * [Reference genomes](https://nf-co.re/usage/reference_genomes)
3. [Running the pipeline](docs/usage.md)
4. [Output and how to interpret the results](docs/output.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)

## Contributions and Support

If you would like to contribute to this pipeline, please see the
[contributing guidelines](.github/CONTRIBUTING.md).

For further information or help, don't hesitate to get in touch on
[Slack](https://nfcore.slack.com/channels/hic).
You can join with [this invite](https://nf-co.re/join/slack).


## Credits

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

## Citation

If you use nf-core/hic for your analysis, please cite it using the following
doi: [10.5281/zenodo.2669513](https://doi.org/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](https://www.biorxiv.org/content/10.1101/610741v1).