Skip to content

paulsengroup/hictk

Repository files navigation

hictk

License docs Ubuntu CI MacOS CI Windows CI Build Dockerfile Fuzzy testing Download from Bioconda

Zenodo DOI


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

This repository hosts hictk: a set of CLI tools to work with Cooler, as well as libhictk: the C++ library underlying hictk.

Python bindings for libhictk are available at paulsengroup/hictkpy.

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

Installing hictk

hictk is developed on Linux and tested on Linux, MacOS and Windows.

hictk can be installed using containers, bioconda or directly from source. Refer to Installation for more information.

Running hictk

hictk provides the following subcommands:

subcommand description
balance Balance HiC matrices using ICE.
convert Convert matrices between .hic and Cooler formats.
dump Write interactions from .hic or Cooler files to the terminal.
fix-mcool Fix corrupted .mcool files.
load Generate a Cooler file from pixels or pairs of interactions in text format.
merge Merge multiple Cooler files using the same reference assembly.
validate Validate Cooler and .hic files.
zoomify Convert single-resolution cooler files to multi-resolution cooler files by coarsening.

Refer to Quickstart (CLI) and CLI Reference for more details.

Using libhictk

libhictk can be installed in various way, including with Conan and CMake FetchContent. Section Quickstart (API) of hictk documentation contains further details on how this can be accomplished.

Quickstart (API) also showcases the basic functionality offered by libhictk. For more complex examples refer to the sample programs under the examples/ folder as well as to the source code of hictk.

The public C++ API of hictk is documented in the C++ API Reference section of hictk documentation.

Citing

If you use hictk in you reaserch, please cite the following publication:

Preprint available soon.

BibTex
@misc{hictk,
author = {Roberto Rossini},
year = {2023},
note = {https://github.com/paulsengroup/hictk},
title = {hictk: blazing fast toolkit to work with .hic and .cool files}
}