LIPIcs.WABI.2024.10.pdf
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b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index
Authors
Lore Depuydt 
,
Luca Renders ,
Simon Van de Vyver ,
Travis Gagie ,
Jan Fostier
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Volume:
24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Series: Leibniz International Proceedings in Informatics (LIPIcs)
Conference: International Workshop on Algorithms in Bioinformatics (WABI) - License:
Creative Commons Attribution 4.0 International license
- Publication Date: 2024-08-26
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Acknowledgements
The authors thank Ben Langmead, Nathaniel Brown, and Mohsen Zakeri for their helpful feedback and suggestions.
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Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, and Jan Fostier. b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 10:1-10:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
https://doi.org/10.4230/LIPIcs.WABI.2024.10
https://doi.org/10.4230/LIPIcs.WABI.2024.10
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 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. 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-index’s favorable memory characteristics. 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. 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.
Subject Classification
ACM Subject Classification
- Applied computing → Bioinformatics
Keywords
- Pan-genomics
- FM-index
- r-index
- Move Structure
- Bidirectional Search
- Approximate Pattern Matching
- Lossless Alignment
- Cache Efficiency
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