Cdbgtricks: Strategies to update a compacted de Bruijn graph - Archive ouverte HAL
Communication Dans Un Congrès Année : 2024

Cdbgtricks: 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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hal-04765742 , version 1 (04-11-2024)

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Khodor Hannoush, Camille Marchet, Pierre Peterlongo. Cdbgtricks: Strategies to update a compacted de Bruijn graph. PSC 2024 - Prague Stringology Conference, Faculty of Information Technology, Czech Technical University in Prague, Aug 2024, Prague (CZ), Czech Republic. pp.1-13, ⟨10.1101/2024.05.24.595676⟩. ⟨hal-04765742⟩
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