Summary:

The VSOB-2 will be devoted to a training course at theoretical and practical levels with the topic: “Genomic analysis of microbial pathogens using illumina and Nanopore technologies”.

1.Course description

Short-read sequencing using Illumina technology has been widely used for whole genome sequencing of microbial pathogens because of the low cost and high accuracy. However, Illumina sequencing-only draft genomes may fail to identify long repeat regions and miss information on certain genomic regions. Long-read sequencing technologies provide greater overlap between reads that enable complete assemblies of microbial genomes. Nanopore sequencing technology can produce reads with an average length greater than 16 Kb which are able to capture long repeat regions. Compared to short-read sequencing, Nanopore sequencing is currently limited by the high error rates. Combination of long-read and short-read sequencing offer a further advantage in generate high-quality whole genome assemblies and will be routinely offered for genome analysis.

The purpose of the workshop is to enhance the knowledge, appreciation, and application of Illumina and Nanopore sequencing related to microbial pathogens. Participants will be able to process raw data from Illumina and Oxford Nanopore sequence data using different bioinformatics tools to produce a high-quality microbial genome sequence.

2. Brief background

Microorganisms can be found in diverse environments including in clinical, environmental or food samples and have the potential to cause disease in plants, animals and humans. Traditionally, microbial pathogens have been detected using culture-based methods or immunological assays. Next-generation sequencing technologies have provided new insights into microbial genome characteristics, molecular mechanisms underlying pathogenicity, as well as the relationship between genotype and phenotype.

3. Course objectives

• For wet-lab, students will be able to explore sequencing protocols and laboratory procedures such as DNA extraction, library preparation, Nanopore sequencing in clinical or food samples; including the need for appropriate and stringent quality control.
• For dry-lab, students are familiar with and can use and apply modern bioinformatics technologies used in genomic research. Processing of raw sequencing data from both short-read and long-read sequencing, including quality control, de novo assembly from raw reads to contigs, genome annotation.