Infectious disease bioinformatics

• 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.

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

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

Lectures and computer-based exercises.