Role of Galaxy in a bioinformatic plant breeding platform

Maillol Vincent, Bacilieri Roberto, Bocs Stéphanie, Boursiquot Jean-Michel, Carrier Gregory, Dereeper Alexis, Droc Gaëtan, Fleury Cécile, Larmande Pierre, Le Cunff Loïc, Péros Jean-Pierre, Pitollat Bertrand, Ruiz Manuel, Sarah Gautier, Sempere Guilhem, Summo Marilyne, This Patrice, Dufayard Jean-François. 2012. Role of Galaxy in a bioinformatic plant breeding platform. In : Galaxy Community Conference GCC2012, Chicago, Etats-Unis, July 25-27 2012. s.l. : s.n., Résumé, 1 p. Galaxy Community Conference, Chicago, États-Unis, 25 July 2012/27 July 2012.

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Abstract : With NGS development, bioinformatics has become central in plant breeding laboratories, and researchers are in need of some autonomy in its use. The Southgreen platform (CIRAD, IRD, INRA) performs bioinformatics analyses for many plant breeding research teams in Montpellier (France), and offers many systems to users: for example GNPAnnot (automatic genomic sequence annotation), Greenphyl (phylogenetic orthology prediction), ESTtik (EST annotation) or the Bacchus analysis pipeline. Most of these systems have been translated into Galaxy workflows. As for the Bacchus pipeline, it has been created at INRA Montpellier (France) to investigate clonal diversity in grapevine genomes. For this task, many softwares have been wrapped in the Galaxy framework. Bacchus can be decomposed in three steps: i) Genome reconstruction, ii) test of reconstruction results, and iii) diversity analysis. This last step is done using SNP's and structural variations. To detect SNP's, the latest Freebayes version was used, while the IDfixe software was developped for structural variation detection. Some of the softwares developped for this pipeline are now used in the international project Grapereseq. Today, the Galaxy framework is widely used by Southgreen plateform users as an alternative to the command line system. In this context, dozens of users have already been trained in Galaxy-using bioinformatics. During weekly collective pair-programming sessions, platform engineers and interested scientists integrate new tools and functionalities.Thus, Galaxy is now a core component of the plant breeding community around the Southgreen platform, and the main access portal for non- bioinformatics specialists to our computing clusters. (Résumé d'auteur)

Classification Agris : F30 - Plant genetics and breeding
C30 - Documentation and information
U10 - Mathematical and statistical methods

Auteurs et affiliations

  • Maillol Vincent, INRA (FRA)
  • Bacilieri Roberto, INRA (FRA)
  • Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
  • Boursiquot Jean-Michel, IFV (FRA)
  • Carrier Gregory, IFV (FRA)
  • Dereeper Alexis, IRD (FRA)
  • Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA)
  • Fleury Cécile
  • Larmande Pierre, IRD (FRA)
  • Le Cunff Loïc, INRA (FRA)
  • Péros Jean-Pierre, INRA (FRA)
  • Pitollat Bertrand, CIRAD-BIOS-UMR AGAP (FRA)
  • Ruiz Manuel, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8153-276X
  • Sarah Gautier, INRA (FRA)
  • Sempere Guilhem, CIRAD-BIOS-UMR AGAP (FRA)
  • Summo Marilyne, CIRAD-BIOS-UMR AGAP (FRA)
  • This Patrice, INRA (FRA)
  • Dufayard Jean-François, CIRAD-BIOS-UMR AGAP (FRA)

Source : Cirad - Agritrop (

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