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

Abstract : 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.
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https://hal-pasteur.archives-ouvertes.fr/pasteur-03516023
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Submitted on : Friday, January 7, 2022 - 5:58:17 AM
Last modification on : Thursday, April 14, 2022 - 5:12:01 PM
Long-term archiving on: : Friday, April 8, 2022 - 6:20:29 PM

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Distributed under a Creative Commons Attribution 4.0 International License

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Nicolas Berthet, Stéphane Descorps-Declère, Andriniaina Andy Nkili-Meyong, Emmanuel Nakouné, Antoine Gessain, et al.. Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data. Biological Research, Sociedad de Biología de Chile, 2016, 49 (1), pp.39. ⟨10.1186/s40659-016-0099-y⟩. ⟨pasteur-03516023⟩

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