ANF MetaBioDiv

Third edition (September 2025)

Welcome to the third edition of the ANF Exploration de la Diversité Taxonomique des Ecosystèmes par Metabarcoding. The aim of this course is to teach you how to run microbial ecology analyses (mostly alpha and beta diversity) from metabarcoding raw sequencing data using R.

Program

You can also find a pdf version of the program here

• Monday 29^th:
  • 09h00: Participants arrival and installation
  • 12h30:
  • 14h00: Training introduction I
  • 14h15: Introduction and R practical by Marc Garel + check technical issues
  • 16h00:
  • 16h15: R practical by Marc Garel + check technical issues
  • 18h00: Seminar “Introduction bonne pratique” - – i.e dépôt github, FAIR principles by M. Garel
  • 19h30: Ice breack, apéritif and diner
• Tuesday 30^th:
  • 08h30: Introduction Metabarcoding to metabarcoding by Loïs Maignien
  • 09h30: Analysing metabarcoding data with dada2 by Charlotte Berthelier
  • 10h15:
  • 10h30: Preprocessing: dada2 by Charlotte Berthelier
  • 12h30:
  • 14h00: Introduction to phyloseq
  • 15h00: Preprocessing: dada2 and Preprocessing: phyloseq by Charlotte Berthelier
  • 16h00:
  • 16h15: Preprocessing: dada2 and Preprocessing: phyloseq by Charlotte Berthelier
  • 18h00: Mise en place des repos de données perso pour ceux qu’il le souhaite outemps libre
  • 19h30:
• Wednesday 1^st:
  • 08h30: Course on alpha diversity 1/2 by Fabrice Armougom and Elsa Mendes
  • 10h15:
  • 10h30: Alpha diversity practical by Fabrice Armougom and Elsa Mendes
  • 12h30:
  • 14h00: Séminaire metabarcoding worklows by Charlotte Berthelier
  • 15h00: Ampliseq configuration workflow by Charlotte Berthelier and Marc Garel
  • 16h00:
  • 16h15: Ampliseq configuration workflow by Charlotte Berthelier and Marc Garel
  • 17h15: Séminaire introduction Long Read by F. Armougom
  • 18h15: Mise en place des repos de données perso pour ceux qu’il le souhaite outemps libre
  • 19h30:
• Thursday 2^nd:
  • 08h30: Course on beta diversity 1/2 by Jean-Christophe Auguet
  • 10h15:
  • 10h30: Beta diversity practical by Jean-Christophe Auguet
  • 12h30:
  • 14h00: Course on beta diversity 2/2 by Jean-Christophe Auguet
  • 15h00: Beta diversity practical by Jean-Christophe Auguet
  • 16h00:
  • 16h15: Beta diversity practical by Jean-Christophe Auguet
  • 18h00: free time
  • 19h30:
• Friday 3^rd:
  • 09h00: À la carte with
  • 12h30:
  • 14h00: End of the course