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 digestion protocols.
Support for other protocols is ongoing.
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)
### Documentation
The nf-core/hic pipeline comes with documentation about the pipeline, found in the `docs/` directory:
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@@ -25,7 +38,5 @@ The nf-core/hic pipeline comes with documentation about the pipeline, found in t
4.[Output and how to interpret the results](docs/output.md)
5.[Troubleshooting](docs/troubleshooting.md)
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### Credits
nf-core/hic was originally written by Nicolas Servant.
