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COV2HTML: A Visualization and Analysis Tool of Bacterial Next Generation Sequencing (NGS) Data for Postgenomics Life Scientists

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  • معلومة اضافية
    • Contributors:
      Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)); Institut Pasteur Paris (IP)-Université Paris Diderot - Paris 7 (UPD7); Pathogénomique mycobactérienne intégrée; Institut Pasteur Paris (IP); Infectiologie et Santé Publique (UMR ISP); Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT); This work was supported by Institut Pasteur and Grant ERA-PTG/SAU/0002/2008 (ERA-NET PathoGenoMics) for Bruno Dupuy and Marc Monot.; European Project: 109584,FCT::,ERA-PTG/2008,ERA-PTG/SAU/0002/2008(2009)
    • بيانات النشر:
      HAL CCSD
      Mary Ann Liebert
    • الموضوع:
      2014
    • Collection:
      Université François-Rabelais de Tours: HAL
    • نبذة مختصرة :
      International audience ; COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results. To demonstrate the scope of COV2HTML, the program was tested with data from two published studies. The first data were from RNA-seq analysis of Campylobacter jejuni, based on comparison of two conditions with two replicates. We were able to recover 26 out of 27 genes highlighted in the publication using COV2HTML. The second data comprised of stranded TSS and RNA-seq data sets on the Archaea Sulfolobus solfataricus. COV2HTML was able to highlight most of the TSSs from the article and allows biologists to visualize both TSS and RNA-seq on the same screen. The strength of the COV2HTML interface is making possible NGS data analysis without software installation, login, or a long training period. A web version is accessible at https://mmonot.eu/COV2HTML/. This website is free and open to users without any login requirement.
    • Relation:
      info:eu-repo/semantics/altIdentifier/pmid/24512253; info:eu-repo/grantAgreement/FCT//109584/EU/Pathogenomic of increased Clostridium difficile virulence/ERA-PTG/SAU/0002/2008; pasteur-01370754; https://hal-pasteur.archives-ouvertes.fr/pasteur-01370754; https://hal-pasteur.archives-ouvertes.fr/pasteur-01370754/document; https://hal-pasteur.archives-ouvertes.fr/pasteur-01370754/file/Monot_COV2HTML.pdf; PRODINRA: 353683; PUBMED: 24512253; PUBMEDCENTRAL: PMC3934542; WOS: 000331798500002
    • الرقم المعرف:
      10.1089/omi.2013.0119
    • Rights:
      http://creativecommons.org/licenses/by-nc-sa/ ; info:eu-repo/semantics/OpenAccess
    • الرقم المعرف:
      edsbas.C88BA419