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
- Mapping using a two steps strategy to rescue reads spanning the ligation sites (bowtie2)
- Detection of valid interaction products
- Duplicates removal
- Create genome-wide contact maps at various resolution
- Contact maps normalization using the ICE algorithm (iced)
- Quality controls and report (MultiQC)
- Addition export for visualisation and downstream analysis (cooler)
Documentation
The nf-core/hic pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
Credits
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.