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

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  • معلومة اضافية
    • Contributors:
      Epidémiologie et Physiopathologie des Virus Oncogènes / Oncogenic Virus Epidemiology and Pathophysiology (EPVO (UMR_3569 / U-Pasteur_3)); Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité); Centre International de Recherches Médicales de Franceville (CIRMF); Bioanalyse génomique (Plate-Forme); Institut Pasteur Paris (IP); Institut Pasteur de Bangui; Réseau International des Instituts Pasteur (RIIP); Environnement et Risques infectieux - Environment and Infectious Risks (ERI); This program was supported by the “Programme Transversal de Recherche” (DEVA No. 246 and CEVACAR n°385) financed by the Institut Pasteur (Paris, France). The funders had no role in study design, data analysis or preparation of the manuscript.; We wish to thank Heïdi Lançon for the English revision of the manuscript.
    • بيانات النشر:
      HAL CCSD
      Sociedad de Biología de Chile
    • الموضوع:
      2016
    • Collection:
      Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe)
    • نبذة مختصرة :
      International audience ; 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.
    • Relation:
      info:eu-repo/semantics/altIdentifier/pmid/27605096; pasteur-03516023; https://pasteur.hal.science/pasteur-03516023; https://pasteur.hal.science/pasteur-03516023/document; https://pasteur.hal.science/pasteur-03516023/file/s40659-016-0099-y.pdf; PUBMED: 27605096; PUBMEDCENTRAL: PMC5015205
    • الرقم المعرف:
      10.1186/s40659-016-0099-y
    • Rights:
      http://creativecommons.org/licenses/by/ ; info:eu-repo/semantics/OpenAccess
    • الرقم المعرف:
      edsbas.63765804