Single-Course English 5 ECTS

Infectious disease bioinformatics

Overall Course Objectives

Whole genome sequencing and bioinformatics has been used successfully in various analyses of infectious diseases such as outbreak investigation and epidemic dynamics. The technology has become so cheap that sequencing platforms are moving into hospitals and food safety laboratories to prevent and control of infectious diseases. The challenge is no longer to generate the sequences, but rather to analyse them and extract the relevant information from the large amounts of sequencing data.

Having followed this course, you will be able to account for the biological and genetic background of different microorganism causing infectious diseases. Further, by using and creating a number of methods, you will learn how to analyse and interpret microbial whole-genome data in relation to infectious disease and food safety issues.

Learning Objectives

  • Be able to use whole genome sequencing data from different sequencing technologies to check for quality, trimming, mapping, alignment and assembly using command-line based bioinformatics methods.
  • Apply command line-based methods to analyse species, sub-typing, identify antimicrobial resistance and other important gene markers.
  • Apply command line-based methods for constructing phylogeny for epidemiological investigations, long-term evolution and large scale phylogeny.
  • Apply command line-based methods to determine major and minor mutations in pathogen genomes.
  • Apply command line-based methods to identify and analyse core-genome, accessory genes and pan-genome.
  • Be able to download and share sequencing data from/to public databases.
  • Evaluate the single components of bioinformatic workflows and pipelines.
  • Apply state-of-the-art methodologies and tools to analyse and interpret genomic data from humans and various reservoirs (animals, food and environment) and prepare such data for epidemiological analyses and modelling.

Course Content

Sequencing technologies, sequencing quality, trimming and assembly using command line tools

Alignment and mapping including handling long read sequencing data

Making Finder tools with example of Identification of species, MLST, antimicrobial resistance, virulence genes and plasmid using command line-based methods

SNP tree construction using command line-based methods and phylogeny visualization

Construction of cgMLST/wgMLST tree and large scale phylogeny

Long term phylogeny using BEAST

Determination of major and minor mutations in sequencing data

Pan-genome analysis including core and accessory genes

Importance of sharing sequencing data, how to download and share sequencing data from/to public databases

Processing, analysing and preparing genomic data for epidemiological analyses and modelling

Recommended prerequisites

23205, Unix/Linux background. Basic understanding of bioinformatics in sequence analysis and infectious disease.

Teaching Method

Lectures and computer-based exercises.



Oral presentation on the last day of the course

See course in the course database.





13 weeks




DTU Lyngby Campus

Course code 23262
Course type Candidate
Semester start Week 5
Semester end Week 19
Days Tues 8-12

7.500,00 DKK