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Introduction to Bacterial Comparative Genomics

This course offers an introduction to microbial genomics analysis.
It includes 5 issues: assembly, genome annotation, circos visualization, pan-genome construction, pan-GWAS.


Linux and knowledge of sequences file formats


  • assemblage de génomes bactériens
  • Identification de scaffolds chromosomique et plasmidique
  • annotation automatique de génomes bactériens avec Prokka
  • visualisation de génomes et annotations avec Circos
  • analyse comparative de 4 génomes avec Roary
  • observation de matrice de présence/absence: notion core-génome, génome accessoire, génome spécifique

Learning objectives

  • Understanding pan-genome concepts
  • Manipulating sequence data on a virtual machine on jupyter environment
  • Handling annotation and visualization tools and be able to analyse your own data
  • Reconstructing pan-genome using multiple bacterial genomes

Training material


  • Alexis Dereeper (AD) -
  • Jean-François Dufayard (JFD) -
  • Nicolas Fernandez (GS) -


Date Location Topics Participants Instructors Links Units
2022 Salle Badiane, Agropolis, Montpellier, France Introduction to Bacterial Genomics 8 AD, JFD, NF   UMR PHIM, AGAP, TransVIH-Mi