Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads

Claire Lemaitre 1, * Liviu Ciortuz 2 Pierre Peterlongo 1
* Auteur correspondant
1 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE, Inria Rennes – Bretagne Atlantique
2 Faculty of Computer Science [Iași]
Abstract : We propose a formal model and an algorithm for detecting inversion breakpoints without a reference genome, directly from raw NGS data. This model is characterized by a fixed size topological pattern in the de Bruijn Graph. We describe precisely the possible sources of false pos- itives and false negatives and we additionally propose a sequence-based filter giving a good trade-off between precision and recall of the method. We implemented these ideas in a prototype called TakeABreak. Ap- plied on simulated inversions in genomes of various complexity (from E. coli to a human chromosome dataset), TakeABreak provided promising results with a low memory footprint and a small computational time.
Type de document :
Communication dans un congrès
Adrian-Horia Dediu; Carlos Martín-Vide; Bianca Truthe. Algorithms for Computational Biology, Jul 2014, Tarragona, Spain. Lecture Notes in Computer Science, 8542, pp.119-130, 2014, 〈10.1007/978-3-319-07953-0_10〉
Liste complète des métadonnées

Littérature citée [12 références]  Voir  Masquer  Télécharger
https://hal.inria.fr/hal-01063157
Contributeur : Pierre Peterlongo <>
Soumis le : lundi 17 novembre 2014 - 09:05:56
Dernière modification le : mercredi 16 mai 2018 - 11:23:35
Document(s) archivé(s) le : mercredi 18 février 2015 - 10:41:55

Fichier

Lemaitre2014_preprint.pdf
Fichiers produits par l'(les) auteur(s)

Identifiants

Collections

INRIA | IRISA | IRISA-D7 | UR1-UFR-ISTIC | UNIV-RENNES

Citation

Claire Lemaitre, Liviu Ciortuz, Pierre Peterlongo. Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads. Adrian-Horia Dediu; Carlos Martín-Vide; Bianca Truthe. Algorithms for Computational Biology, Jul 2014, Tarragona, Spain. Lecture Notes in Computer Science, 8542, pp.119-130, 2014, 〈10.1007/978-3-319-07953-0_10〉. 〈hal-01063157v3〉

Exporter

BibTeX TEI DC DCterms EndNote

Partager

Métriques

Consultations de la notice

477

Téléchargements de fichiers

136

Contact


archive-ouverte@inria.fr