Toward perfect reads

Antoine Limasset 1, 2 Jean-François Flot 1 Pierre Peterlongo 2
2 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA_D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : We propose a new method to correct short reads using de Bruijn graphs, and implement it as a tool called Bcool. As a first step, Bcool constructs a corrected compacted de Bruijn graph from the reads. This graph is then used as a reference and the reads are corrected according to their mapping on the graph. We show that this approach yields a better correction than kmer-spectrum techniques, while being scalable, making it possible to apply it to human-size genomic datasets and beyond. The implementation is open source and available at github.com/Malfoy/BCOOL
Type de document :
Pré-publication, Document de travail
RECOMB 2018 Submission. 2017
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https://hal.inria.fr/hal-01644163
Contributeur : Pierre Peterlongo <>
Soumis le : mercredi 22 novembre 2017 - 08:49:30
Dernière modification le : mercredi 16 mai 2018 - 11:24:15

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  • HAL Id : hal-01644163, version 1
  • ARXIV : 1711.03336

Citation

Antoine Limasset, Jean-François Flot, Pierre Peterlongo. Toward perfect reads. RECOMB 2018 Submission. 2017. 〈hal-01644163〉

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