Huey, Jack DAbdennur, Nezar2024-08-302024-08-302024-06-03Huey JD, Abdennur N. Bigtools: a high-performance BigWig and BigBed library in Rust. Bioinformatics. 2024 Jun 3;40(6):btae350. doi: 10.1093/bioinformatics/btae350. PMID: 38837370; PMCID: PMC11167208.1367-481110.1093/bioinformatics/btae35038837370https://hdl.handle.net/20.500.14038/53741Motivation: The BigWig and BigBed file formats were originally designed for the visualization of next-generation sequencing data through a genome browser. Due to their versatility, these formats have long since become ubiquitous for the storage of processed sequencing data and regularly serve as the basis for downstream data analysis. As the number and size of sequencing experiments continues to accelerate, there is an increasing demand to efficiently generate and query BigWig and BigBed files in a scalable and robust manner, and to efficiently integrate these functionalities into data analysis environments and third-party applications. Results: Here, we present Bigtools, a feature-complete, high-performance, and integrable software library for generating and querying both BigWig and BigBed files. Bigtools is written in the Rust programming language and includes a flexible suite of command line tools as well as bindings to Python. Availability and implementation: Bigtools is cross-platform and released under the MIT license. It is distributed on Crates.io, Bioconda, and the Python Package Index, and the source code is available at https://github.com/jackh726/bigtools.enCopyright The Author(s) 2024. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.; Attribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/genomicsbioinformaticssoftware libraryJournal ArticleBioinformatics (Oxford, England)