Abstract
In this paper, we introduce the Conway-Bromage-Lyndon (CBL) structure, a compressed, dynamic and exact method for representingk-mer sets. Originating from Conway and Bromage’s concept, CBL innovatively employs the smallest cyclic rotations ofk-mers, akin to Lyndon words, to leverage lexico-graphic 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 existingk-mer set methods, particularly in dynamic scenarios. Unique to this work, CBL stands out as the only known exactk-mer structure offering in-place set operations. Its different combined abilities position it as a flexible Swiss knife structure fork-mer set management. Availability:https://github.com/imartayan/CBL
Publisher
Cold Spring Harbor Laboratory