Title :

Strategies to update a compacted de Bruijn graph

Author(s) :

Hannoush, Khodor [Auteur correspondant]
Scalable, Optimized and Parallel Algorithms for Genomics [GenScale]
Marchet, Camille [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Peterlongo, Pierre [Auteur]
Scalable, Optimized and Parallel Algorithms for Genomics [GenScale]

Conference title :

SeqBIM 2024 - Journées annuelles du groupe de travail SeqBIM (Séquences en Bioinformatique, Informatique et Mathématiques)

City :

Rennes

Country :

France

Start date of the conference :

2024-11-28

Book title :

SeqBIM 2024

Publication date :

2024-11-19

HAL domain(s) :

Informatique [cs]/Bio-informatique [q-bio.QM]
Informatique [cs]/Algorithme et structure de données [cs.DS]

English abstract : [en]

<div><p>We propose Cdbgtricks, a new method for updating a compacted de Bruijn graph when addingnovel sequences, such as full genomes. Our method indexes the graph, enabling to identify in constanttime the location (unitig ...
Show more ><div><p>We propose Cdbgtricks, a new method for updating a compacted de Bruijn graph when addingnovel sequences, such as full genomes. Our method indexes the graph, enabling to identify in constanttime the location (unitig and offset) of any k-mer. The update operation that we propose also updatesthe index. Our results show that Cdbgtricks is faster than Bifrost and GGCAT. We benefit from theindex of the graph to provide new functionalities, such as reporting the subgraph that share a desiredpercentage of k-mers with a query sequence with the ability to query a set of reads. The open-sourceCdbgtricks software is available at https://github.com/khodor14/Cdbgtricks.</p></div>Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL