Bacterial Comparative Genomics

• Provide participants with the technical proficiency required to process and analyze read data for bacterial genomes.
• Enable participants to perform de novo assembly, genome annotation, and comparative genomic analyses using state-of-the-art bioinformatics tools.
• Foster an understanding of bacterial genome evolution, genetic diversity, and functional genomics.
• Familiarize participants with tools for identifying antimicrobial resistance genes and conducting pangenome analyses to elucidate bacterial genome dynamics.
• Introduce participants to Comparative Genomics Webservers for further exploration and analysis of bacterial genomes.

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

• Undergraduate degree in Microbiology, Bioinformatics, Genetics, or related fields.
• Professionals in the biotechnology, pharmaceutical, or healthcare industries.
• Individuals with a keen interest in genomics and bacterial research.