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 = {Rossini, Roberto and Paulsen, Jonas},
    title = "{hictk: blazing fast toolkit to work with .hic and .cool files}",
    journal = {Bioinformatics},
    volume = {40},
    number = {7},
    pages = {btae408},
    year = {2024},
    month = {06},
    issn = {1367-4811},
    doi = {10.1093/bioinformatics/btae408},
    url = {https://doi.org/10.1093/bioinformatics/btae408},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/40/7/btae408/58385157/btae408.pdf},
}

Table of contents¶

Installation

FAQ

Frequently Asked Questions (FAQ)

Getting Started

How-Tos

Telemetry

Telemetry