Conway-Bromage-Lyndon (CBL): an exact, dynamic representation ofk-mer sets

In this paper, 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: https://github.com/imartayan/CBL