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Biological Research

, 49:39

First Online: 07 September 2016Received: 30 October 2015Accepted: 25 August 2016DOI: 10.1186-s40659-016-0099-y

Cite this article as: Berthet, N., Descorps-Declère, S., Nkili-Meyong, A.A. et al. Biol Res 2016 49: 39. doi:10.1186-s40659-016-0099-y

Abstract

BackgroundNew sequencing technologies have opened the way to the discovery and the characterization of pathogenic viruses in clinical samples. However, the use of these new methods can require an amplification of viral RNA prior to the sequencing. Among all the available methods, the procedure based on the use of Phi29 polymerase produces a huge amount of amplified DNA. However, its major disadvantage is to generate a large number of chimeric sequences which can affect the assembly step. The pre-process method proposed in this study strongly limits the negative impact of chimeric reads in order to obtain the full-length of viral genomes.

FindingsThree different assembly softwares ABySS, Ray and SPAdes were tested for their ability to correctly assemble the full-length of viral genomes. Although in all cases, our pre-processed method improved genome assembly, only its combination with the use of SPAdes allowed us to obtain the full-length of the viral genomes tested in one contig.

ConclusionsThe proposed pipeline is able to overcome drawbacks due to the generation of chimeric reads during the amplification of viral RNA which considerably improves the assembling of full-length viral genomes.

KeywordsRNA viral genome Next generation sequencing SPAdes Assembling genome Amplification with phi29 polymerase AbbreviationsNGSnew generation sequencing

cDNAcomplementary DNA

BLASTbasic local alignment search tools

TStargeted sequence

USuntargeted sequence

BESTBruijn, van Aardenne-Ehrenfest, Smith and Tutte

EMCVencephalomyocarditis virus

OLCoverlap layout consensus

Electronic supplementary materialThe online version of this article doi:10.1186-s40659-016-0099-y contains supplementary material, which is available to authorized users.

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Autor: Nicolas Berthet - Stéphane Descorps-Declère - Andriniaina Andy Nkili-Meyong - Emmanuel Nakouné - Antoine Gessain - Jean-C

Fuente: https://link.springer.com/







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