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Ten steps to get started in Genome Assembly and Annotation

Dominguez del Angel Victoria, Hjerde Erik, Sterck Lieven, Capella-Gutierrez Salvadors, Notredame Cederic, Vinnere Pettersson Olga, Amselem Joelle, Bouri Laurent, Bocs Stéphanie, Klopp Christophe, Gibrat Jean-François, Vlasova Anna, Leskosek Brane L., Soler Lucile, Binzer-Panchal Mahesh, Lantz Henrik. 2018. Ten steps to get started in Genome Assembly and Annotation. F1000Research, 7:148

Journal article ; Autre type d'article ; Article de revue à comité de lecture Revue en libre accès total
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Abstract : As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR).

Mots-clés libres : Genome assembly, Genome annotation, FAIR data, NGS Workflows, DNA

Classification Agris : F30 - Plant genetics and breeding
L10 - Animal genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Agence(s) de financement européenne(s) : European Commission

Programme de financement européen : H2020

Projet(s) de financement européen(s) : ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences

Auteurs et affiliations

  • Dominguez del Angel Victoria, CNRS (FRA)
  • Hjerde Erik, The Arctic University of Norway (NOR)
  • Sterck Lieven, University of Ghent (BEL)
  • Capella-Gutierrez Salvadors, Spanish National Bioinformatics Institute (ESP)
  • Notredame Cederic, Centre for Genomic Regulation (ESP)
  • Vinnere Pettersson Olga, Uppsala University (SWE)
  • Amselem Joelle, INRA (FRA)
  • Bouri Laurent, CNRS (FRA)
  • Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
  • Klopp Christophe, INRA (FRA)
  • Gibrat Jean-François, CNRS (FRA)
  • Vlasova Anna, Universitat Pompeu Fabra (ESP)
  • Leskosek Brane L., INRA (FRA)
  • Soler Lucile, Uppsala University (SWE)
  • Binzer-Panchal Mahesh, Uppsala University (SWE)
  • Lantz Henrik, Uppsala University (SWE) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/590547/)

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