First version of nf-core Hi-C pipeline based on the HiC-Pro pipeline.
The current version supports most protocols including Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C or HiChip data.
- Automatic detection and generation of annotation files
- Two-steps alignment of raw sequencing reads
- Reads filtering and detection of valid interaction products
- Generation of raw contact matrices for a set of resolutions
- Normalization of the contact maps using the ICE algorithm
- Generation of cooler file for visualization on higlass
- Quality report based on HiC-Pro MultiQC module