Introduction#

hictk is a blazing fast toolkit to work with .hic and .cool files.

hictk is capable of reading and writing files in .cool, .mcool, .scool and .hic format (including hic v9).

Documentation formats#

You are reading the HTML version of the documentation. An alternative PDF version is also available.

Installation#

hictk is developed on Linux and tested on Linux, MacOS and Windows. CLI tools can be installed in several different ways. Refer to Installation for more details.

hictk can be compiled on most UNIX-like systems (including many Linux distributions and MacOS) as well as Windows. See the build instructions for more details.

hictk can be used from languages other than C++ through the following bindings:

Python bindings through hictkpy
R bindings through hictkR

How to cite this project?#

Please use the following BibTeX template to cite hictk in scientific discourse:

@article {hictk,
        author = {Roberto Rossini and Jonas Paulsen},
        title = {hictk: blazing fast toolkit to work with .hic and .cool files},
        elocation-id = {2023.11.26.568707},
        year = {2023},
        doi = {10.1101/2023.11.26.568707},
        publisher = {Cold Spring Harbor Laboratory},
        URL = {https://www.biorxiv.org/content/early/2023/11/27/2023.11.26.568707},
        eprint = {https://www.biorxiv.org/content/early/2023/11/27/2023.11.26.568707.full.pdf},
        journal = {bioRxiv}
}

If you use hictk convert to convert .[m]cool files to .hic format you should also cite JuicerTools or HiCTools.

Table of contents#

Installation

Introduction

Tutorials