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@apeltzer apeltzer released this May 6, 2019

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
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