Instructor
Ahmed M. Moustafa
Teaching Assistants
Daniel P. Morreale (Dan)
Qianxuan She (Sean)
Erin Marie Theiller (Erin)
All sessions were recorded and they are available on YouTube.
- Why is it important to learn microbial genomics?
- Aim
- Tips
- Knowledge Map
- Session 1: Unix
- Why would I need to use command-line?
- How to open a terminal?
- Make a New Folder
- Running Commands
- Useful Unix Commands
- Getting Information About Commands
- Useful Command-Line Shortcuts and Keystrokes
- Wildcards
- Command Line Arguments
- Standard Input and Output Redirection
- GitHub
- Conda
- Bioconda
- Text Editors
- Further Readings
- Problem Set 1
- Session 2: Quality Control
- Problem Set 2
- Session 3: Assembly
- Problem Set 3
- Session 4: Annotation
- Problem Set 4
- Session 5: Blast database and Typing/MLST
- Problem Set 5
- Session 6: Reference based analysis
- Problem Set 6
- Session 7: Pangenome analysis
- Problem Set 7
- Session 8: Panallelome analysis
- Problem Set 8
- Session 9: Metagenomics
- Problem Set 9
- Session 10: Kmer analysis and Recombination Detection
- Problem Set 10
- Session 11: Phylogenetics
- Problem Set 11
- Session 12: Workflows! What is next?
- Session 13: Graduation Project