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# 
**Analysis of Chromosome Conformation Capture data (Hi-C)**.
[](https://github.com/nf-core/hic/actions)
[](https://github.com/nf-core/hic/actions)
[](https://www.nextflow.io/)
[](https://bioconda.github.io/)
[](https://hub.docker.com/r/nfcore/hic)
[](https://nfcore.slack.com/channels/hic)
## Introduction
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 containers making installation trivial and results highly reproducible.
## Quick Start
1. Install [`nextflow`](https://nf-co.re/usage/installation)
2. Install either [`Docker`](https://docs.docker.com/engine/installation/) or [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
3. Download the pipeline and test it on a minimal dataset with a single command:
```bash
nextflow run nf-core/hic -profile test,<docker/singularity/conda/institute>
```
> Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
4. Start running your own analysis!
<!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
```bash
nextflow run nf-core/hic -profile <docker/singularity/conda/institute> --input '*_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 which you can read at [https://nf-core/hic/docs](https://nf-core/hic/docs) or find in the [`docs/` directory](docs).
<!-- TODO nf-core: Add a brief overview of what the pipeline does and how it works -->
nf-core/hic was originally written by Nicolas Servant.
## 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 the [Slack `#hic` channel](https://nfcore.slack.com/channels/hic) (you can join with [this invite](https://nf-co.re/join/slack)).
## Citation
<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi. -->
<!-- If you use nf-core/hic for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
You can cite the `nf-core` publication as follows:
> **The nf-core framework for community-curated bioinformatics pipelines.**
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
> ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)