Learning Pathway Bacterial comparative genomics
Date: No date given
This learning path aims to teach you how to analyze bacterial genomes, starting with genome retrieval from NCBI and GTDB. The workflow will include quality control (CheckM2), dereplication (dRep), and pangenomic analysis (PPanGolin). Functional and structural annotation will be performed, with a focus on identifying mobile genetic elements and antimicrobial resistance genes. Phylogenetic analysis will compare core genome trees and presence-absence pangenome trees to reveal complementary evolutionary insights.
Keywords: bacteria, comparative genomics, microgalaxy, pangenome, phylogeny
Learning objectives:
- Evaluate the annotation
- Get information about ARGs
- Process the outputs to formate them for visualization needs
- Run a series of tool to annotate a draft bacterial genome for different types of genomic components
- Run a series of tool to assess the presence of antimicrobial resistance genes (ARG)
- Visualize a draft bacterial genome and its annotations
- Visualize the ARGs and plasmid genes in their genomic context
- to do
Event types:
- Workshops and courses
Sponsors: ABRomics, Avans Hogeschool, ELIXIR Europe, Institut Français de Bioinformatique
Scientific topics: Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements, Public health and epidemiology, Infectious disease, Antimicrobial resistance, Phylogeny
Activity log
