Depuydt, LoreLoreDepuydtRenders, LucaLucaRendersVan de Vyver, SimonSimonVan de VyverVeys, LennartLennartVeysGagie, TravisTravisGagieFostier, JanJanFostier2025-08-232025-08-232025-AUG 11748-7188WOS:001547855700001https://imec-publications.be/handle/20.500.12860/46099Background Due to the increasing availability of high-quality genome sequences, pan-genomes are gradually replacing single consensus reference genomes in many bioinformatics pipelines to better capture genetic diversity. Traditional bioinformatics tools using the FM-index face memory limitations with such large genome collections. Recent advancements in run-length compressed indices like Gagie et al.’s r-index and Nishimoto and Tabei’s move structure, alleviate memory constraints but focus primarily on backward search for MEM-finding. Arakawa et al.’s br-index initiates complete approximate pattern matching using bidirectional search in run-length compressed space, but with significant computational overhead due to complex memory access patterns. Results We introduce b-move, a novel bidirectional extension of the move structure, enabling fast, cache-efficient, lossless approximate pattern matching in run-length compressed space. It achieves bidirectional character extensions up to 7 times faster than the br-index, closing the performance gap with FM-index-based alternatives. For locating occurrences, b-move performs and operations up to 7 times faster than the br-index. At the same time, it maintains the favorable memory characteristics of the br-index, for example, all available complete E. coli genomes on NCBI’s RefSeq collection can be compiled into a b-move index that fits into the RAM of a typical laptop. Conclusions b-move proves practical and scalable for pan-genome indexing and querying. We provide a C++ implementation of b-move, supporting efficient lossless approximate pattern matching including locate functionality, available at https://github.com/biointec/b-move under the AGPL-3.0 licenseJournal article10.1186/s13015-025-00281-xWOS:001547855700001READ ALIGNMENTMEDLINE:40796877