A bacterial genome assembly and annotation laboratory using a virtual machine

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Rising antibiotic-resistant bacterial infections necessitate novel approaches.
• Genomic analysis is crucial for understanding bacterial virulence and resistance.
• Bioinformatics expertise is increasingly vital in biological sciences.

Purpose of the Study:

• To design and implement a hands-on workshop for university students.
• To teach essential bioinformatics skills for bacterial genome assembly and analysis.
• To provide practical experience with command-line tools and different sequencing technologies.

Main Methods:

• Utilized virtual machines with Linux operating systems for a standardized learning environment.
• Employed both Illumina (short-read) and Nanopore (long-read) raw sequencing data.
• Taught genome assembly using short, long, and hybrid approaches, including quality assessment and annotation.

Main Results:

• Students gained practical skills in bacterial genome assembly and quality control.
• The workshop effectively demonstrated the comparative advantages of short, long, and hybrid assembly methods.
• Participants learned to analyze pathogenicity and antibiotic/phage resistance from genomic data.

Conclusions:

• The developed workshop equips students with critical bioinformatics skills for tackling antibiotic resistance.
• Hands-on training in genome assembly and analysis is essential for future biological scientists.
• This educational module provides a comprehensive approach to understanding bacterial genomics.