Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data

BACKGROUND: New 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 bas...

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Autores principales:	Berthet,Nicolas, Descorps-Declère,Stéphane, Nkili-Meyong,Andriniaina Andy, Nakouné,Emmanuel, Gessain,Antoine, Manuguerra,Jean-Claude, Kazanji,Mirdad
Lenguaje:	English
Publicado:	Sociedad de Biología de Chile 2016
Materias:	RNA viral genome Next generation sequencing SPAdes Assembling genome Amplification with phi29 polymerase
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602016000100039
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spelling	oai:scielo:S0716-976020160001000392016-12-01Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing dataBerthet,NicolasDescorps-Declère,StéphaneNkili-Meyong,Andriniaina AndyNakouné,EmmanuelGessain,AntoineManuguerra,Jean-ClaudeKazanji,Mirdad RNA viral genome Next generation sequencing SPAdes Assembling genome Amplification with phi29 polymerase BACKGROUND: New 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. FINDINGS: Three 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. CONCLUSIONS: The 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.info:eu-repo/semantics/openAccessSociedad de Biología de ChileBiological Research v.49 20162016-01-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602016000100039en10.1186/s40659-016-0099-y
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	RNA viral genome Next generation sequencing SPAdes Assembling genome Amplification with phi29 polymerase
spellingShingle	RNA viral genome Next generation sequencing SPAdes Assembling genome Amplification with phi29 polymerase Berthet,Nicolas Descorps-Declère,Stéphane Nkili-Meyong,Andriniaina Andy Nakouné,Emmanuel Gessain,Antoine Manuguerra,Jean-Claude Kazanji,Mirdad Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data
description	BACKGROUND: New 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. FINDINGS: Three 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. CONCLUSIONS: The 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.
author	Berthet,Nicolas Descorps-Declère,Stéphane Nkili-Meyong,Andriniaina Andy Nakouné,Emmanuel Gessain,Antoine Manuguerra,Jean-Claude Kazanji,Mirdad
author_facet	Berthet,Nicolas Descorps-Declère,Stéphane Nkili-Meyong,Andriniaina Andy Nakouné,Emmanuel Gessain,Antoine Manuguerra,Jean-Claude Kazanji,Mirdad
author_sort	Berthet,Nicolas
title	Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data
title_short	Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data
title_full	Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data
title_fullStr	Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data
title_full_unstemmed	Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data
title_sort	improved assembly procedure of viral rna genomes amplified with phi29 polymerase from new generation sequencing data
publisher	Sociedad de Biología de Chile
publishDate	2016
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602016000100039
work_keys_str_mv	AT berthetnicolas improvedassemblyprocedureofviralrnagenomesamplifiedwithphi29polymerasefromnewgenerationsequencingdata AT descorpsdeclerestephane improvedassemblyprocedureofviralrnagenomesamplifiedwithphi29polymerasefromnewgenerationsequencingdata AT nkilimeyongandriniainaandy improvedassemblyprocedureofviralrnagenomesamplifiedwithphi29polymerasefromnewgenerationsequencingdata AT nakouneemmanuel improvedassemblyprocedureofviralrnagenomesamplifiedwithphi29polymerasefromnewgenerationsequencingdata AT gessainantoine improvedassemblyprocedureofviralrnagenomesamplifiedwithphi29polymerasefromnewgenerationsequencingdata AT manuguerrajeanclaude improvedassemblyprocedureofviralrnagenomesamplifiedwithphi29polymerasefromnewgenerationsequencingdata AT kazanjimirdad improvedassemblyprocedureofviralrnagenomesamplifiedwithphi29polymerasefromnewgenerationsequencingdata
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Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data

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