ArticleBioinformatics (Oxford, England)2024
hictk: blazing fast toolkit to work with .hic and .cool files.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Identification of differential topologically associating domains from low sequencing depth and pseudobulk chromatin contact maps.Genome research · 2026Article
- UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.Genome biology · 2026Article
- Chromosome-Level Genome and Organ-Specific Transcriptome of Alnus glutinosa Uncover Lineage-Specific Innovations in Root Nodule Symbiosis.Plant, cell & environment · 2026Article
- Jointly-hic: joint decomposition of contact frequency maps captures salient features of genome architecture across tissues and development.Genome biology · 2026Article
- UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.bioRxiv : the preprint server for biology · 2026Article
- Loss of multilevel 3D genome organization during breast cancer progression.Genome research · 2026Article
- A split luciferase biosensing platform for detection and imaging of chromatin loops in individual live cells.Nucleic acids research · 2025Article
- The 3D nuclear position and compartmentalization of genes prime their response to mechano-confinement.bioRxiv : the preprint server for biology · 2025Article
- StripePy: fast and robust characterization of architectural stripes.Bioinformatics (Oxford, England) · 2025Article
- Predicting 3D Chromatin Interactions Using Transformer-Enhanced Deep Learning Models.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
2 authors.
Funding
Abstract
motivationHi-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.
resultsWe 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. AVAILABILITY AND IMPLEMENTATION: 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.