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# nf-core/hic: Changelog
* Support 'N' base motif in restriction/ligation sites
* Support multiple restriction enzymes/ligattion sites (comma separated) (#31)
* Fix bug for reads extension _1/_2 (#30)
* Update manual (#28)
First version of nf-core Hi-C pipeline which is a Nextflow implementation of the [HiC-Pro pipeline](https://github.com/nservant/HiC-Pro/).
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](https://higlass.io/)
* Quality report based on HiC-Pro MultiQC module