BWR-finder: BWT-based de novo interspersed repeat detection for gigantic genomes

We developed BWR-finder (Burrows–Wheeler transform-based Repeat finder), a new software tool for database-free detection of interspersed repeats in large genomes of tens of gigabases. BWR-finder employs a BWT-based seed-and-extend repeat detection algorithm and parallelized extension computation, improving both runtime and memory usage. In benchmarks using the rice and human genomes, BWR-finder reduced runtime compared with RepeatModeler2, HiTE, and REPrise, and reduced memory usage compared with HiTE and REPrise, while maintaining high nucleotide-level repeat detection sensitivity. BWR-finder also enabled whole-genome repeat detection in genomes larger than 10 Gb and identified candidate repeat regions and repeat consensus sequences in the 20.3-Gb Pleurodeles waltl genome that were not associated with existing repeat annotations or libraries.