phancanhtrinh/bacterial_wgs_training

In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.

Bacterial WGS training

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.

Slides

Day 1

• Exercise 0 -- Download pdf
• Talk 1: Linux environment review.
• Exercise 1 -- Download pdf
• Talk 2 and 3: Massive sequencing of bacterial genomes. State-of-the-art. & Bacterial genomes sequencing. Applications.

Day 2

• Talk 4: The computing revolution in Biosciences. Nextflow and Singularity introduction.

• Exercise 2 -- Download pdf

• Talk 5: Quality analysis and control of HTS data

• Talk 6: Bacterial genomes assembly

• Exercise 3 -- Download pdf

Day 3

• Talk 7: Mapping against reference genome and Variant Calling.

• Talk 8: SNP matrix and phylogenetics.

• Exercise 4 -- Download pdf

Day 4

• Talk 9: Typing based on allelic profile or gene-by-gene

• Talk 10: Gene-by-gene WGS analysis

• Exercise 5 -- Download pdf

Day 5

• Talk 11: Sequence annotation
• Talk 12: [Genome characterization, Resistance and Virulence genes]
• Exercise 6 -- Download pdf