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Graph analysis of fragmented long-read bacterial genome assemblies

Pierre Marijon 1 Rayan Chikhi 2 Jean-Stéphane Varré 2
1 BONSAI - Bioinformatics and Sequence Analysis
Université de Lille, Sciences et Technologies, Inria Lille - Nord Europe, CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189, CNRS - Centre National de la Recherche Scientifique
Abstract : Motivation Long-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. Results We 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.
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https://hal.archives-ouvertes.fr/hal-02167175
Contributor : Jean-Stéphane Varré <>
Submitted on : Thursday, June 27, 2019 - 3:08:06 PM
Last modification on : Friday, January 8, 2021 - 3:14:06 PM

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Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré. Graph analysis of fragmented long-read bacterial genome assemblies. Bioinformatics, Oxford University Press (OUP), 2019, ⟨10.1093/bioinformatics/btz219⟩. ⟨hal-02167175⟩

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