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Bacterial comparative genomics#

Course overview#

GitHub repository 8 - 9 June, 2023

This course aims at discovering the main bioinformatics for comparing bacterial genomes, from pairwise comparison to a large scale pan-genome analysis.

Course content and learning outcomes#

The following topics and tools are covered in the course: Genome assembly, Identification of plasmid scaffolds, Annotation, circos visualization, ANI, pan-gene atlas, pan-GWAS, pangenome graph

Application#

By accepting to participate in the course, you agree to follow the Code of Conduct.

Schedule#

8 June

  • Genome assembly
  • Identification of plasmid scaffolds
  • Annotation (structural and functional annotation) of bacterial genomes
  • Circos representation of genomes
  • Pairwise comparison of genomes (ANI)

9 June

  • Comparative analysis of gene content
  • PAV (Presence/Absence Variation))
  • Pan-genome/core-genome aspects
  • pan-GWAS
  • Pan-genome graph approach

Location#

This course round is given on site. It will take place in the Badiane room at Agropolis.

Course material#

here lists all the information you need before the course starts.

Teachers#

  • Alexis Dereeper (course leader)
  • Jacques Dainat
  • Florian Charriat
  • Antoni Exbrayat

Contact#

To contact us, please send a mail using the contact form available here.