Strategies to update a compacted de Bruijn graph - Inria - Institut national de recherche en sciences et technologies du numérique
Communication Dans Un Congrès Année : 2024

Strategies to update a compacted de Bruijn graph

Résumé

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.

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Dates et versions

hal-04861344 , version 1 (02-01-2025)

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  • HAL Id : hal-04861344 , version 1

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Khodor Hannoush, Camille Marchet, Pierre Peterlongo. Strategies to update a compacted de Bruijn graph. SeqBIM 2024, Nov 2024, Rennes, France. ⟨hal-04861344⟩
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