Analysis of Chromosome Conformation Capture data (Hi-C)
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.
- 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)
iii. Download the pipeline and test it on a minimal dataset with a single command
Please check nf-core/configs 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
singularityand set the appropriate execution settings for your local compute environment.
iv. Start running your own analysis!
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
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
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.
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:
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.