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.
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 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.
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 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}
}