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.

Agenda

Day 1

• Talk 1 and 2: Massive sequencing of bacterial genomes. State-of-the-art. & Bacterial genomes sequencing. Applications.
• Talk 3: The computing revolution in Biosciences. Nextflow and Singularity introduction.
• Talk 4: Linux environment review.
• Exercise 0 -- Download pdf
• Exercise 1 -- Download pdf
• Exercise 2 -- Download pdf

Day 2

• Talk 5: Quality analysis and control of HTS data
• Talk 6: Bacterial genomes assembly
• Talk 7: Sequence annotation
• Exercise 3 -- Download pdf

Day 3

• Talk 8: Mapping against reference genome and Variant Calling.
• Talk 9: SNP matrix and phylogenetics.
• Exercise 4 -- Download pdf

Day 4

• Talk 10: Typing based on allelic profile or gene-by-gene
• Talk 11: Gene-by-gene WGS analysis
• Exercise 5 -- Download pdf
• Exercise 6 -- Download pdf