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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) -
  • Jacques Dainat (JD) -
  • Antoni Exbrayat (AE) -
  • Florian Charriat (FC) -
  • Jean-Francois Dufayard (JFD) -


Date Location Topics Participants Instructors Links Units
2022 Zoom from Montpellier, France Bacterial Comparative Genomics   AD,NF,JFD   UMR PHIM, AGAP, TransVIHMi
2023 Montpellier, France Bacterial Comparative Genomics   AD,JD,AE,FC   UMR PHIM, Mivegec, ASTRE