Fast, parallel, and cache-friendly suffix array construction

• Published in: Algorithms for molecular biology Vol. 19; no. 1; p. 16
• Main Authors: Khan, Jamshed, Rubel, Tobias, Molloy, Erin, Dhulipala, Laxman, Patro, Rob
• Format: Journal Article
• Language: English
• Published: London BioMed Central 28.04.2024; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Arrays; Bioinformatics; Biomedical and Life Sciences; Cellular and Medical Topics; Computational Biology/Bioinformatics; Computer peripherals; Construction; Data structures; Genomes; Genomics; Hierarchies; Indexing; Life Sciences; Longest common prefix; Methods; Parallel algorithms; Performance indices; Physiological; Strings; Suffix array; Data structures; Parallel algorithms; Suffix array; Longest common prefix; Indexing
• ISSN: 1748-7188; 1748-7188
• DOI: 10.1186/s13015-024-00263-5

Purpose String indexes such as the suffix array ( sa ) and the closely related longest common prefix ( lcp ) array are fundamental objects in bioinformatics and have a wide variety of applications. Despite their importance in practice, few scalable parallel algorithms for constructing these are known, and the existing algorithms can be highly non-trivial to implement and parallelize. Methods In this paper we present caps-sa , a simple and scalable parallel algorithm for constructing these string indexes inspired by samplesort and utilizing an LCP-informed mergesort. Due to its design, caps-sa has excellent memory-locality and thus incurs fewer cache misses and achieves strong performance on modern multicore systems with deep cache hierarchies. Results We show that despite its simple design, caps-sa outperforms existing state-of-the-art parallel sa and lcp -array construction algorithms on modern hardware. Finally, motivated by applications in modern aligners where the query strings have bounded lengths, we introduce the notion of a bounded-context sa and show that caps-sa can easily be extended to exploit this structure to obtain further speedups. We make our code publicly available at https://github.com/jamshed/CaPS-SA .