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 and .hic files, as well as libhictk: the C++ library underlying hictk.
Python bindings for libhictk are available at paulsengroup/hictkpy, while R bindings are published at paulsengroup/hictkR.
hictk is capable of reading files in .cool, .mcool, .scool and .hic format (including hic v9) as well as writing .hic, .cool and .mcool files.
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.
hictk provides the following subcommands:
| subcommand | description |
|---|---|
| balance | Balance Hi-C files using ICE, SCALE, or VC. |
| convert | Convert Hi-C files between different formats. |
| dump | Read interactions and other kinds of data from .hic and Cooler files and write them to stdout. |
| fix-mcool | Fix corrupted .mcool files. |
| load | Build .cool and .hic files from interactions in various text formats. |
| merge | Merge multiple Cooler or .hic files into a single file. |
| metadata | Print file metadata to stdout. |
| rename-chromosomes | Rename chromosomes found in a Cooler file. |
| validate | Validate .hic and Cooler files. |
| zoomify | Convert single-resolution Cooler and .hic files to multi-resolution by coarsening. |
Refer to Quickstart (CLI) and CLI Reference for more details.
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.
If you use hictk in you research, please cite the following publication:
Roberto Rossini, Jonas Paulsen, hictk: blazing fast toolkit to work with .hic and .cool files Bioinformatics, Volume 40, Issue 7, July 2024, btae408, https://doi.org/10.1093/bioinformatics/btae408
BibTex
@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},
}