hictk

Blazing fast toolkit to work with .hic and .cool files

https://github.com/paulsengroup/hictk

Science Score: 67.0%

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CITATION.cff file
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Scientific vocabulary similarity
Low similarity (7.9%) to scientific vocabulary

Keywords

3d-genomics bioinformatics cli-application conversion cooler cxx cxx-library cxx17 genomics hi-c hic hictk

Last synced: 4 months ago · JSON representation ·

Repository

Blazing fast toolkit to work with .hic and .cool files

Basic Info

Host: GitHub
Owner: paulsengroup
License: mit
Language: C++
Default Branch: main
Homepage: https://hictk.readthedocs.io
Size: 10.3 MB

Statistics

Stars: 38
Watchers: 2
Forks: 1
Open Issues: 13
Releases: 21

Topics

3d-genomics bioinformatics cli-application conversion cooler cxx cxx-library cxx17 genomics hi-c hic hictk

Created over 2 years ago · Last pushed 5 months ago

Metadata Files

Readme License Citation

hictk

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

The toolkit consists of a native CLI application and a C++ library running on Linux, macOS, and Windows.\ hictk offers native IO support for Cooler and .hic files, meaning that its implementation is independent of that of cooler, JuicerTools, or straw.

hictk can also be accessed from several programming languages using one of the following libraries:

hictkpy - Python bindings for hictk: read and write .cool and .hic files directly from Python
hictkR - R bindings for hictk: read .cool and .hic files directly from R
libhictk - The native C++ library that underlies hictk

Features

Supported formats

The CLI application and C++ library are capable of reading and writing files in the following formats:

| Format | Revision | Read | Write | | ------ | ---------- | ---- | --------------- | | .cool | v1-3 (all) | ✅ | ✅ ¹ | | .mcool | v1-2 (all) | ✅ | ✅ ² | | .scool | v1 (all) | ✅ | ✅ ³ | | .hic | v6-9 | ✅ | ✅ ⁴ |

¹ v3 only\ ² v2 only\ ³ libhictk only\ ⁴ v9 only

Supported operations

Seamless conversion between Cooler and .hic formats (from hic to cool and vice versa)
Uniform interface to query interaction matrices
High performance and low memory requirements (see benchmarks in the Supplementary Text from our paper)
Easy access to file metadata
Create files from interaction pairs or pre-binned interaction counts (e.g. 4DN-DCIC pairs or BEDPE/bedGraph2)
Merge interactions from multiple files into a single file (also supports merging files in different formats)
Detect (and when possible fix) corrupted files
Balance interaction matrices using ICE, SCALE, or VC
Create multi-resolution files suitable for visualization with JuiceBox and HiGlass

All the above operations can be performed on both Cooler and .hic files and yield identical results.

Installation

hictk can be installed using containers, bioconda, Conan, or directly from source.\ Refer to the Installation section in the documentation for more information.

Quickstart

hictk (CLI)

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 the Quickstart (CLI) and CLI Reference sections in the documentation for more details.

libhictk

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

Quickstart (API) also demonstrates 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 or any of its language bindings in your 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

```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}, } ```

Owner

Name: paulsengroup
Login: paulsengroup
Kind: organization

Repositories: 3
Profile: https://github.com/paulsengroup

Citation (CITATION.cff)

# Copyright (C) 2024 Roberto Rossini <roberros@uio.no>
#
# SPDX-License-Identifier: MIT

cff-version: 1.2.0
message: 'If you use this software, please cite it using the metadata from this file.'
authors:
  - given-names: Roberto
    family-names: Rossini
    orcid: 'https://orcid.org/0000-0003-3096-1470'
    email: roberros@uio.no
    affiliation: 'Department of Biosciences, University of Oslo'
title: hictk
abstract: 'Blazing fast toolkit to work with .hic and .cool files.'
doi: '10.5281/zenodo.8214220'
url: 'https://github.com/paulsengroup/hictk'
repository-code: 'https://github.com/paulsengroup/hictk'
repository-artifact: 'https://github.com/paulsengroup/hictk/pkgs/container/hictk'
type: software
license: MIT
keywords:
  - bioinformatics
  - cxx
  - conversion
  - cooler
  - cli-application
  - hic
  - cxx17
  - cxx-library
  - hictk
preferred-citation:
  type: article
  authors:
  - given-names: Roberto
    family-names: Rossini
    orcid: 'https://orcid.org/0000-0003-3096-1470'
    email: roberros@uio.no
    affiliation: 'Department of Biosciences, University of Oslo'
  - given-names: Jonas
    family-names: Paulsen
    orcid: 'https://orcid.org/0000-0002-7918-5495'
    email: jonas.paulsen@ibv.uio.no
    affiliation: 'Department of Biosciences, University of Oslo'
  doi: '10.1093/bioinformatics/btae408'
  url: 'https://academic.oup.com/bioinformatics/article/40/7/btae408/7698028'
  journal: 'Bioinformatics'
  year: 2024
  month: 06
  title: 'hictk: blazing fast toolkit to work with .hic and .cool files'
  abstract: >
    Hi-C is gaining prominence as a method for mapping genome organization.
    With declining sequencing costs and a growing demand for higher-resolution data, efficient tools for processing Hi-C datasets at different resolutions are crucial.
    Over the past decade, the .hic and Cooler file formats have become the de-facto standard to store interaction matrices produced by Hi-C experiments in binary format.
    Interoperability issues make it unnecessarily difficult to convert between the two formats and to develop applications that can process each format natively.

    We developed hictk, a toolkit that can transparently operate on .hic and .cool files with excellent performance.
    The toolkit is written in C++ and consists of a C++ library with Python and R bindings as well as CLI tools to perform common operations directly from the shell, including converting between .hic and .mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries.
    We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication.

    The hictk library, Python bindings and CLI tools are released under the MIT license as a multi-platform application available at github.com/paulsengroup/hictk.
    Pre-built binaries for Linux and macOS are available on bioconda.
    Python bindings for hictk are available on GitHub at github.com/paulsengroup/hictkpy, while R bindings are available on GitHub at github.com/paulsengroup/hictkR.

GitHub Events

Total

Create event: 132
Issues event: 18
Release event: 9
Watch event: 12
Delete event: 126
Issue comment event: 130
Push event: 385
Pull request review event: 1
Pull request review comment event: 2
Pull request event: 236

Last Year

Create event: 132
Issues event: 18
Release event: 9
Watch event: 12
Delete event: 126
Issue comment event: 130
Push event: 385
Pull request review event: 1
Pull request review comment event: 2
Pull request event: 236

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 23
Total pull requests: 186
Average time to close issues: about 1 month
Average time to close pull requests: 4 days
Total issue authors: 9
Total pull request authors: 4
Average comments per issue: 0.52
Average comments per pull request: 0.67
Merged pull requests: 124
Bot issues: 0
Bot pull requests: 33

Past Year

Issues: 7
Pull requests: 109
Average time to close issues: about 2 months
Average time to close pull requests: 4 days
Issue authors: 5
Pull request authors: 3
Average comments per issue: 1.29
Average comments per pull request: 0.64
Merged pull requests: 62
Bot issues: 0
Bot pull requests: 31

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Pull Request Authors

robomics (238)
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Phlya (1)

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enhancement (66) dependencies (38) CI (25) bug (23) github_actions (18) testing (16) documentation (12) python (2)

Dependencies

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Dockerfile docker

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Data

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Open Source Science

hictk

Science Score: 67.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

hictk

Features

Supported formats

Supported operations

Installation

Quickstart

hictk (CLI)

libhictk

Citing

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

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