About this Course
This course will cover the topic of Whole genome sequencing (WGS) of bacterial genomes which is becoming more and more relevant for the medical sector. WGS technology and applications are high on international political agenda, as the classical methods are being replaced by WGS technology and therefore bioinformatic tools are extremely important for allowing the people working in this sector to be able to analyze the data and obtain results that can be interpreted and used for different purposes. The course will give the learners a basis to understand and be acquainted with WGS applications in surveillance of bacteria including species identification, typing and characterization of antimicrobial resistance and virulence traits as well as plasmid characterization. It will also give the opportunity to learners to learn about online tools and what they can be used for through demonstrations on how to use some of these tools and exercises to be solved by learners with use of freely available WGS analysis tools . By the end of this course you should be able to: 1. Describe the general Principles in typing of Bacteria 2. Give examples of the applications of Whole Genome Sequencing to Surveillance of bacterial pathogens and antimicrobial resistance 3. Apply genomic tools for sub-typing and surveillance 4. Define the concept of Next-Generation Sequencing and describe the sequencing data from NGS 5. Describe how to do de novo assembly from raw reads to contigs 6. Enumerate the methods behind the tools for species identification, MLST typing and resistance gene detection 7. Apply the tools for species identification, MLST typing and resistance gene detection in real cases of other bacterial and pathogen genomes. 8. Describe the methods behind the tools for Salmonella and E.coli typing, plasmid replicon detection and plasmid typing 9. Utilize the tools for Salmonella and E.coli typing, plasmid replicon detection and plasmid typing in real cases of other bacterial and pathogen genomes. 10. Explain the concept and be able to use the integrated bacterial analysis pipeline for batch analysis and typing of genomic data 11. Demonstrate how to construct phylogenetic tree based on SNPs 12. Apply the phylogenetic tool to construct phylogenetic trees and explain the relatedness of bacterial or pathogen strains 13. Describe how to create your own sequence database 14. Utilize the MyDbFinder tool to detect genetic markers of interest from whole genome sequencing
Globe

100% online course

Start instantly and learn at your own schedule.
Beginner Level

Beginner Level

Clock

Approx. 10 hours to complete

Suggested: This course will run over 5 weeks, 2-3 hours a week
Comment Dots

English

Subtitles: English
Globe

100% online course

Start instantly and learn at your own schedule.
Beginner Level

Beginner Level

Clock

Approx. 10 hours to complete

Suggested: This course will run over 5 weeks, 2-3 hours a week
Comment Dots

English

Subtitles: English

Syllabus - What you will learn from this course

1

Section
Clock
1 hour to complete

Module 1

Welcome and introduction to typing of bacteria and use of Whole genome sequencing applied to surveillance of bacterial pathogens and antimicrobial resistance...
Reading
3 videos (Total 32 min), 1 quiz
Video3 videos
General Principles of typing of bacteria12m
Surveillance of Antimicrobial Resistance using whole genome sequencing12m
Quiz1 practice exercises
Module 120m

2

Section
Clock
1 hour to complete

Module 2

Introduction to Next Generation sequencing...
Reading
3 videos (Total 37 min), 1 quiz
Video3 videos
Introduction to Next-Generation sequencing (NGS)19m
De novo assembly- from raw reads to contigs: assembler tool description and application5m
Quiz1 practice exercises
Module 230m

3

Section
Clock
1 hour to complete

Module 3

Whole genome sequencing tools- demonstration of analysis tools for species identification, MLST typing and finding resistance genes...
Reading
3 videos (Total 30 min), 1 quiz
Video3 videos
MLST Typing: MLST tool description and applications8m
Resistance gene detection: Resfinder tool description and applications12m
Quiz1 practice exercises
Module 320m

4

Section
Clock
1 hour to complete

Module 4

Whole genome sequencing tools- demonstration of analysis tools for Serotyping of Salmonella and Escherichia coli strains , and finding plasmid replicons...
Reading
3 videos (Total 24 min), 1 quiz
Video3 videos
E. coli serotype identification: serotype finder tool description and applications6m
Plasmid replicon identification and plasmid typing12m
Quiz1 practice exercises
Module 420m

5

Section
Clock
2 hours to complete

Module 5

Whole genome sequencing tools- demonstration of analysis tools for multiple analyzes, phylogenetic tree building and finding genetic markers from self-made databases and Summative Tutorial exercise...
Reading
5 videos (Total 42 min), 1 reading, 2 quizzes
Video5 videos
Phylogenetic relatedness: CSI Phylogeny tool description and applications13m
Multipurpose detection of genetic markers- My Db finder tool description and applications10m
Tutorial3m
Final Remarks and perspectives1m
Reading1 readings
Text with Link to files to be used in tutorial10m
Quiz2 practice exercises
Module 520m
Tutorial final Quiz20m
4.6
Direction Signs

50%

started a new career after completing these courses
Briefcase

83%

got a tangible career benefit from this course
Money

29%

got a pay increase or promotion

Top Reviews

By ABDec 17th 2017

I loved the course. I lerned how to use different tools to understant a DNA information, with a lot of practical exercises. I can wait the course of metagenomics.

By VMJun 3rd 2018

Me gustaron los video que van directo al fundamento de cada herramienta, y lo mejor es que el curso también se enfoca en la aplicación de lo enseñado. Gracias

Instructors

About Technical University of Denmark (DTU)

DTU focuses on research in technical and natural sciences that contributes to the development of society. As an industrially orientated university, our goal is to supply high-level international research based on combining theory with constructing models and empirical methods....

Frequently Asked Questions

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