GIA: A genome interval arithmetic toolkit for high performance interval set operations

Motivation This study addresses the pressing need for efficient interval techniques in processing vast genomic datasets, such as those generated by ChIP-seq, RNA-seq, and whole-genome sequencing. Intervals are critical in characterizing biological features, necessitating streamlined interval manipulation for meaningful insights. Existing tools often struggle with memory and runtime requirements when managing extensive genomic region arithmetic. Results The study introduces GIA (Genomic Interval Arithmetic) and BEDRS, a novel command-line tool and a rust library that significantly enhance the performance of genomic interval analysis. GIA outperforms existing tools like BEDOPS, BEDTools, and GenomicRanges by a factor of 2x to 20x across a range of operations. These advances enable researchers to perform genomic interval operations more efficiently, drastically reducing computational time and resource requirements in high-throughput genomic sequencing analysis. Availability and Implementation - https://github.com/noamteyssier/gia - https://github.com/noamteyssier/bedrs