Course English

Whole genome sequencing analysis for microbial diagnostic, identification and cluster analysis

Whole genome sequencing can be used for e.g. outbreak investigations, antimicrobial resistance monitoring, characterization of microorganisms, and the diagnostic of microbe in clinical setting.

Whole genome sequencing (WGS) is being used/could be used in several applications for different purposes which include, e.g. outbreak investigations (strain characterization and clustering analyses), antimicrobial resistance (AMR) monitoring (strain characterization including detection of resistance genes, plasmids and AMR prediction), also for regulated products, including the characterization of microorganisms used as or producers of food or feed additives and or/ biopesticides (species identification, strain characterization, detection of AMR, virulence and toxin production and other metabolites), and the diagnostic of microbe in clinical setting.

A student who has met the objectives of the course will be able to:

Explain and discuss different methodologies for sequencing, data processing, experimental design
Explain and discuss the quality of sequencing data, quality parameters, calculation of average read depth/minimum read depth, assembling.
Apply web-based bioinformatic methods to analyse WGS data (e.g. gene finding), SNPs and gene by gene based clustering)
Apply the WGS analysis in risk assessment, surveillance, diagnostic and characterization for microorganisms, (e.g. taxonomy/identification of the microorganisms, antimicrobial resistance and virulence characterization, outbreak investigations).
Explain and discuss the process, the type of bioinformatic tools available
Explain and discuss what information we may retrieve from the sequence analysis, gene detection, sequence alignment tools
Explain and discuss the advantages and limitations in using the WGS approach as well as metagenomic approach.
Explain and discuss the critical aspects to focus when using WGS and main uncertainties associated.

WGS fundamentals: what is WGS, main use, sequencing strategies, sample/library preparation, experimental design, different types of bioinformatics tools (online), new developments, data sharing, etc. WGS Microbial: what is the process, which are the tools considering, for e.g.: trimming, short and long read assembly, quality assessment, species identification, subtyping using MLST, antimicrobial resistance, plasmid, SNPs detection, gene by gene analysis, cluster analysis, data visualisation, metagenomic analysis and incorporation of WGS and Machine learning for risk assessment and microbial characterization.

Understand the principle and analytic tools for WGS analysis
Be able to use different WGS tools for analyzing bacterial sequencing data
Be able to apply WGS analysis in their routine workflow

Any researchers/scientists from various industries such as hospital, food industry and, governmental

agency related to food safety.

The course is for 4 days. It consists of lectures and hands-on computer exercises, with an interactive and learner-centered approach, with a right balance between fundamentals notions, theory and practical elements. Most of the bioinformatics tools used in the training are web-based tools. Therefore, there is no need to have a bioinformatic background to attend the course. In addition, you will use your own computer during the course for computer exercises.

Where is the lecture conducted?

DTU Lyngby Campus

When does the course start and take place:

DTU Lyngby Campus, 1-4 June 2026

The duration of the course/programme:

4 days

Admission requirements:

Basic knowledge on molecular biology and microbiology

NB!

DTU PhD students must register for these courses through the Study Planner.