Hictk: blazing fast toolkit to work with .hic and .cool files.

ABSTRACT:

Motivation

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.

Results

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 wel

SUBMITTER: Rossini R 

PROVIDER: S-EPMC11216752 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature