hich aims to be the most general-purpose Hi-C processing pipeline.

• Population (bulk) and single cell
• Targeted and non-targeted
• Unmodified and bisulfite-converted DNA
• Compatible with major formats: open2c (.cool, .mcool, .scool), Juicer (.hic), and HiCPro(.validPairs, .allValidPairs)
• Advanced QC tools come built in
• Powerful new features for homogenizing coverage when merging replicates or pseudobulking
• Containerized for automated and reproducible installation of dependencies
• Built on Nextflow, permitting use locally or on HPC environments
• Simple to use. Some experiments can be processed with the simple command "nextflow run hich.nf"!

The hich logo is a DNA knot made with optical tweezers. Hi-C and other assays detect loops, compartments, and other 3D features of chromatin conformation.

Bao, Xiaoyan R., Heun Jin Lee, and Stephen R. Quake. "Behavior of complex knots in single DNA molecules." Physical review letters 91.26 (2003): 265506.