Cdbgtricks: Strategies to update a compacted de Bruijn graph

Overview & Synopsis

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 share 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 .