Program

  • November 7th
      • 13h00–14h00: Participants welcome
    • 14h00–14h30: Pierre Peterlongo (GenScale Rennes) 
      • Presentation of the workshop and of the Colib’read main objectives and ideas.
      • slides
    • 14h30–15h30: Rayan Chikhi (Bonsai Lille)
      • Graph representations of reference-free sequencing data
      • slides
    • 15h30–16h00: Break
    • 16h00–16h30: Dominique Lavenier (GenScale Rennes)
      • Genome Analysis Tool Box: designing fast and efficient NGS tools
      • slides
    • 16h30–17h15: Éric Rivals (MAB Montpellier)
      • Hybrid and non hybrid error correction for long reads: LoRDEC and LoRMA
      • slides
    • 17h15–18h00: Stephanie D’Souza (Boston University, USA) – Success Story
      • Hybrid assembly of a draft genome sequence for the Egyptian fruit bat, an important viral reservoir – abstract
    • 18h00–18h30: Claire Lemaitre (GenScale Rennes) 
      • Reference-free variant discovery : looking for bubbles in a haystack
      • slides
    • 18h30–……….: Cocktail
  • November 8th
    • 09h30–10h00: Pierre Peterlongo (GenScale Rennes) 
      • DiscoSnp++: genomic small variant discovery with no reference genome and modest ressources.
      • slides
    • 10h00–10h30: Gilles Boutet (INRA IGEPP Rennes) – Success Story
      • WGGBS in pea, a successful discoSnp use without genome reduction and at low sequence coverage
      • slides
    • 10h30–11h00: Hélène Lopez-Maestre (LBBE Lyon)
      • SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
      • slides
    • 11h00–11h30: Break
    • 11h30–12h00: Claude Rispe & Pierre Charrier (Oniris Nantes) – Success Story
      • Using KisSplice to detect SNPs or alternative splicing events from RNAseq data sets: the examples of grapevine phylloxera and ticks
      • slides_rispe
      • slides_charrier
    • 12h00–12h30: Clara Benoit-Pilven (LBBE Lyon) 
      • Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data
      • slides
    • 12h30–14h00: Lunch – (on-spot buffet)
    • 14h00–15h00: Vincent Lacroix (LBBE Lyon) & Pierre Peterlongo (GenScale Rennes) – Live Demo
    • 15h00–15h30: Break
    • 15h30–16h30: colib’read team Live roundtable discussion
      Participants are invited to contact us (pierre.peterlongo@inria.fr) if they want to discuss a specific problem close to the Colib’read framework. You will be offered the opportunity to make a two-slides presentation, raising up your question.
    • Future of the project and conclusions.