In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.
The material includes slides with theory concepts and a bunch of practical exercises using nextflow and singularity, focusing on the interpretation of results.
- Talk 1: Massive sequencing of bacterial genomes. State-of-the-art
- Talk 2: Linux environment review.
- Exercise 0 -- Download pdf
- Talk 3: Shell usage and basic commands.
- Talk 4: The computing revolution in Biosciences. Nextflow and Singularity introduction.
- Exercise 1 -- Download pdf
- Talk 4: Bacterial genomes sequencing. Applications.
- Talk 5: Quality analysis and control of HTS data
- Talk 6: Bacterial genomes assembly
- Exercise 2 -- Download pdf
- Talk 9: Typing based on allelic profile or gene-by-gene
- Talk 10: Gene-by-gene WGS analysis
- Talk 11: Sequence annotation
- Talk 12: Genome characterization. Resistance and virulence