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 .
Fichier principal
Vignette du fichier
2024.05.24.khodor.full.pdf (864.73 Ko) Télécharger le fichier
Origine Fichiers produits par l'(les) auteur(s)

Dates et versions

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

Identifiants

Citer

Khodor Hannoush, Camille Marchet, Pierre Peterlongo. Cdbgtricks: Strategies to update a compacted de Bruijn graph. PSC2024, Faculty of Information Technology, Czech Technical University in Prague, Aug 2024, Prague (CZ), Czech Republic. ⟨10.1101/2024.05.24.595676⟩. ⟨hal-04765742⟩
0 Consultations
0 Téléchargements

Altmetric

Partager

More