Cdbgtricks: Strategies to update a compacted de Bruijn graph

Abstract We propose Cdbgtricks, a new method for updating a compacted de Bruijn graph when adding novel sequences, such as full genomes. Our method indexes the graph, enabling to identify in constant time the location (unitig and offset) of any k-mer. The update operation that we propose also updates the index. Our results show that Cdbgtricks is faster than Bifrost and GGCAT. We benefit from the index of the graph to provide new functionalities, such as reporting the subgraph that shares a desired percentage of k-mers with a query sequence with the ability to query a set of reads. The open-source Cdbgtricks software is available at https://github.com/khodor14/Cdbgtricks. Competing Interest Statement The authors have declared no competing interest. Footnotes khodor.hannoush{at}inria.fr camille.marchet{at}univ-lille.fr pierre.peterlongo{at}inria.fr The query section in the manuscript has been revised as well as the corresponding experiments.