Graph analysis of fragmented long-read bacterial genome assemblies

Marijon, Pierre; Chikhi, Rayan; Varré, Jean-Stéphane

Type de document :

Article dans une revue scientifique: Article original

DOI :

10.1093/bioinformatics/btz219

Titre :

Graph analysis of fragmented long-read bacterial genome assemblies

Auteur(s) :

Marijon, Pierre [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Chikhi, Rayan [Auteur]

Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Varré, Jean-Stéphane [Auteur]

Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]

Titre de la revue :

Bioinformatics

Éditeur :

Oxford University Press (OUP)

Date de publication :

2019-03-27

ISSN :

1367-4803

Discipline(s) HAL :

Informatique [cs]/Bio-informatique [q-bio.QM]

Résumé en anglais : [en]

MotivationLong-read genome assembly tools are expected to reconstruct bacterial genomes nearly perfectly, however they still produce fragmented assemblies in some cases. It would be beneficial to understand whether these ...
Lire la suite >MotivationLong-read genome assembly tools are expected to reconstruct bacterial genomes nearly perfectly, however they still produce fragmented assemblies in some cases. It would be beneficial to understand whether these cases are intrinsically impossible to resolve, or if assemblers are at fault, implying that genomes could be refined or even finished with little to no additional experimental cost.ResultsWe propose a set of computational techniques to assist inspection of fragmented bacterial genome assemblies, through careful analysis of assembly graphs. By finding paths of overlapping raw reads between pairs of contigs, we recover potential short-range connections between contigs that were lost during the assembly process. We show that our procedure recovers 45% of missing contig adjacencies in fragmented Canu assemblies, on samples from the NCTC bacterial sequencing project. We also observe that a simple procedure based on enumerating weighted Hamiltonian cycles can suggest likely contig orderings. In our tests, the correct contig order is ranked first in half of the cases and within the top-3 predictions in nearly all evaluated cases, providing a direction for finishing fragmented long-read assemblies.Lire moins >

Langue :

Anglais

Comité de lecture :

Oui

Audience :

Internationale

Vulgarisation :

Non

Collections :

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

Source :

Harvested from HAL

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http://pdfs.semanticscholar.org/03f2/27538744ef2250274348832826c4918cac91.pdf
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