Module 1:
- Installing genomics tools with Conda
- Obtaining reads Data
- Perform QC and Trimming of Data
- Perform de novo assembly using spades
Module 2:
- Polish the draft assembly using pilon
- Reordering contigs against a reference genome using ragtag
- Multi-locus sequence typing
- Annotate the draft genome using prokka
Module 3:
- Look for antimicrobial resistance genes using abricate
- Perform Pangenome Analysis
- Overview of Comparative Genomics Webserver like BV-BRC
Requirements:
• Working knowledge of Linux OS system is a must for the program
• PC with Linux operating system or Microsoft Windows Subsystem for Linux (see this link: https://www.freecodecamp.org/news/how-to-install-wsl2-windows-subsystem-for-linux-2-on-windows-10/)
• Install conda. For installing conda in the Windows sub-system see the link: https://medium.com/@parham.motameni/install-conda-on-wsl2-2e76d1e03229