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 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
- Talk 5: Quality analysis and control of HTS data
- Talk 6: Bacterial genomes assembly
- Talk 7: Sequence annotation
- Exercise 3 -- Download pdf
- Talk 8: Mapping against reference genome and Variant Calling.
- Talk 9: SNP matrix and phylogenetics.
- Exercise 4 -- Download pdf
- 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