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The South Green Bioinformatics platform, a comprehensive resource for crop genomics

Ruiz Manuel, Dereeper Alexis, Droc Gaëtan, Sarah Gautier, Tranchant-Dubreuil Christine, Dufayard Jean François, Guignon Valentin, Hamelin Chantal, De Lamotte Frédéric, Larmande Pierre, Sabot François, Sempere Guilhem, Summo Marilyne, Pitollat Bertrand, This Dominique, Bocs Stéphanie, Hueber Yann, El Hassouni Nordine, Martin Guillaume, Gkanogiannis Anestis, Ravel Sébastien, Monat Cécile, Tando Ndomassi, Rouard Mathieu. 2017. The South Green Bioinformatics platform, a comprehensive resource for crop genomics. In : Proceedings X-Meeting 2017. s.l. : s.n., 1 p. International Conference of the AB3. 13, São Pedro, Brésil, 4 October 2017/6 October 2017.

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Additional Information : Manuel Ruiz est l'expert invité du Cirad

Abstract : Analysis and visualization of massive genomics datasets are an ongoing trend in plant sciences. The South Green Bioinformatics platform provides an ecosystem of tools that were originally developed as independent entities to fulfill the need for specific projects or crops, but have evolved over time to generic tools to comprehensively study crop genomics. We have built a large panel of public information systems dedicated to specialized datasets (markers, genes, gene families, transcriptomes, genotypes, phenotypes, etc.) and crop-specific resources called Genome Hubs. Target users of bioinformatic analytical workflows are usually divided between people who use command-line and those who do not. We addressed both categories by offering complementary solutions, like Galaxy-based and command-line applications. Various groups used the South Green infrastructure to obtain their data and results, and were able to publish high-quality biological information, on Coffee genome, Banana, Cocoa, African rice or large transcriptome resources. Tools developed for these studies are adaptable to a wide range of other organisms.

Auteurs et affiliations

  • Ruiz Manuel, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8153-276X
  • Dereeper Alexis
  • Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA)
  • Sarah Gautier, INRA (FRA)
  • Tranchant-Dubreuil Christine, IRD (FRA)
  • Dufayard Jean François, CIRAD-BIOS-UMR AGAP (FRA)
  • Guignon Valentin, Bioversity International (FRA)
  • Hamelin Chantal, CIRAD-BIOS-UMR AGAP (FRA)
  • De Lamotte Frédéric, INRA (FRA)
  • Larmande Pierre, IRD (FRA)
  • Sabot François, IRD (FRA)
  • Sempere Guilhem, CIRAD-BIOS-UMR INTERTRYP (FRA)
  • Summo Marilyne, CIRAD-BIOS-UMR AGAP (FRA)
  • Pitollat Bertrand, CIRAD-BIOS-UMR AGAP (FRA)
  • This Dominique, Montpellier SupAgro (FRA)
  • Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
  • Hueber Yann, Bioversity International (ITA)
  • El Hassouni Nordine, INRA (FRA)
  • Martin Guillaume, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-1801-7500
  • Gkanogiannis Anestis, CIAT (BRA)
  • Ravel Sébastien, CIRAD-BIOS-UMR BGPI (FRA)
  • Monat Cécile, IRD (FRA)
  • Tando Ndomassi, IRD (FRA)
  • Rouard Mathieu, Bioversity International (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/591684/)

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