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Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets
Igor Martayan1, Bastien Cazaux1, Antoine Limasset1
1Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, Lille, F-59000, France.
Summary:
In this article, we introduce the Conway-Bromage-Lyndon (CBL) structure, a compressed, dynamic and exact method for representing k-mer sets. Originating from Conway and Bromage's concept, CBL innovatively employs the smallest cyclic rotations of k-mers, akin to Lyndon words, to leverage lexicographic redundancies. In order to support dynamic operations and set operations, we propose a dynamic bit vector structure that draws a parallel with Elias-Fano's scheme. This structure is encapsulated in a Rust library, demonstrating a balanced blend of construction efficiency, cache locality, and compression. Our findings suggest that CBL outperforms existing dynamic k-mer set methods. Unique to this work, CBL stands out as the only known exact k-mer structure offering in-place set operations. Its different combined abilities position it as a flexible Swiss knife structure for k-mer set management.
Availability And Implementation:
https://github.com/imartayan/CBL.
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