Introduction to Bacterial Comparative GenomicsThis course offers an introduction to microbial genomics analysis. It includes 5 issues: assembly, genome annotation, circos visualization, pan-genome construction, pan-GWAS. |
Prerequisites
Linux and knowledge of sequences file formats
Program
- 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
Instructors
- Alexis Dereeper (AD) - alexis.dereeper@ird.fr
- Jacques Dainat (JD) - jacques.dainat@ird.fr
- Antoni Exbrayat (AE) - antoni.exbrayat@cirad.fr
- Florian Charriat (FC) - florian.charriat@cirad.fr
- Jean-Francois Dufayard (JFD) - jean-francois.dufayard@cirad.fr
Trainings
| 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 |