CHANGELOG.md



To find the state of this project's repository at the time of any of these versions, check out the tags.


nf-core/hic: Changelog

v1.1dev

Support 'N' base motif in restriction/ligation sites
Support multiple restriction enzymes/ligattion sites (comma separated) (#31)
Add --saveInteractionBAM option
Add DOI (#29)
Fix bug for reads extension _1/_2 (#30)
Update manual (#28)


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