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CHANGELOG.md 862 B

nf-core/hic: Changelog

v1.0 - 2019-05-06

First version of nf-core Hi-C pipeline which is a Nextflow implementation of the HiC-Pro pipeline. Note that all HiC-Pro functionalities are not yet all implemented. The current version supports most protocols including Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C or HiChip data.

In summary, this version allows :

  • Automatic detection and generation of annotation files based on igenomes if not provided.
  • 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