PT - JOURNAL ARTICLE AU - Martayan, Igor AU - Cazaux, Bastien AU - Limasset, Antoine AU - Marchet, Camille TI - Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of <em>k</em>-mer sets AID - 10.1101/2024.01.29.577700 DP - 2024 Jan 01 TA - bioRxiv PG - 2024.01.29.577700 4099 - http://biorxiv.org/content/early/2024/03/25/2024.01.29.577700.short 4100 - http://biorxiv.org/content/early/2024/03/25/2024.01.29.577700.full AB - 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/CBLCompeting Interest StatementThe authors have declared no competing interest.