Materials

Materials
Pathogen of Interest
- Pathogen genomic surveillances
Introduction to NGS
- Introduction to NGS
- Conda Environments
Quality Control of Raw Reads
- Quality Control of Raw Reads
- Trimming to Retain High Quality Data
Genome Assembly
- De novo Assembly
- Quality Control of Assembly File
Classification
- Taxonomy: Kraken2
- MLST-Multilocus Sequence Typing
Annotation
- Genome Annotation with Prokka
- AMR and Virulence Factors
Phylogenetics
- Pangenome Analysis
- Phylogenetics

Materials

Detailed course materials can be found in this section, including exercises to practice. If you are a self-learner, and working on your local desktop/laptop make sure to check the

Conda installation guideline for setting up WSL (only if working in Windows OS) and Conda environment.
Unix Cheat Sheet for navigating basic shell commands.

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Pathogen genomic surveillances

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