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bioRxiv · 10.1101/2024.05.30.596587

b-move: faster bidirectional character extensions in a run-length compressed index

Depuydt, L.·Renders, L.·Van de Vyver, S.·Veys, L.·Gagie, T.·Fostier, J.
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Abstract

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 Tabeis 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. We introduce b-move, a novel bidirectional extension of the move structure, enabling fast, cache-efficient bidirectional character extensions in run-length compressed space. It achieves bidirectional character extensions up to 8 times faster than the br-index, closing the performance gap with FM-index-based alternatives, while maintaining the br-indexs favorable memory characteristics. For example, all available complete E. coli genomes on NCBIs RefSeq collection can be compiled into a b-move index that fits into the RAM of a typical laptop. Thus, 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 license. FundingLore Depuydt: PhD Fellowship FR (1117322N), Research Foundation - Flanders (FWO) Luca Renders: PhD Fellowship SB (1SE7822N), Research Foundation - Flanders (FWO) Travis Gagie: NSERC Discovery Grant RGPIN-07185-2020 to Travis Gagie and NIH grant R01HG011392 to Ben Langmead

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Depuydt, L., Renders, L., Van de Vyver, S., Veys, L., Gagie, T., Fostier, J.. 2024-06-02. b-move: faster bidirectional character extensions in a run-length compressed index. https://doi.org/10.1101/2024.05.30.596587

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