nfcore/hic repository overview

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

⁠Introduction

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 either Docker⁠ or Singularity⁠ for full pipeline reproducibility (please only use Conda⁠ as a last resort; see docs⁠)

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

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

iv. Start running your own analysis!

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

See usage docs⁠ 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
2. Pipeline configuration
   • Local installation⁠
   • Adding your own system config⁠
   • Reference genomes⁠
3. Running the pipeline⁠
4. Output and how to interpret the results⁠
5. Troubleshooting⁠

The nf-core/hic pipeline comes with documentation about the pipeline which you can read at https://nf-core/hic/docs⁠ or find in the docs/ directory⁠.

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

⁠Credits

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.

For further information or help, don't hesitate to get in touch on the Slack #hic channel⁠ (you can join with this invite⁠).

⁠Citation

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 publication as follows: