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


Technical University of Denmark


General course objectives:
Currently, in research institutes, hospitals and industries, the use of whole genome sequencing (WGS) is an area of key interest for scientific officers/researcher. 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. It has been recognised the need to increase the knowledge on WGS data analysis so that scientific officers/researchers can enhance their critical ability and competence to use WGS data for specifically in the microbial area. The course is for 4 days including a submission of report after the course (report is only for enrolled PhD student who receives grade with pass and not pass). It shall consist on lectures and hands-on computer exercise, with an interactive and learner-centred approach, with a right balance between fundamentals notions, theory and practical elements. Most of the bioinformatics tools used in the training is web-based tools. Therefore, there is no need to have bioinformatic background to attend the course. In addition, you will use your own computer during the course for the computer exercises. While this is a stand-alone course, it comes after an accompanying wet-lab course. The wet lab course can be found with course number: 23842.

Learning objectives:
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.

Contents:
• 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.

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Course organizer
Pimlapas
Place/Venue
Anker Engelunds Vej 1
City
2800 Kgs. Lyngby
Country
Denmark
Workload
1.5
Link
http://kurser.dtu.dk/course/23841