Whole genome sequencing of bacterial genomes - tools and applications
Offered By
Whole genome sequencing of bacterial genomes - tools and applications
Technical University of Denmark (DTU)
About this Course
4.6
157 ratings
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
Skills you will gain
GenomeMicrobiologyAntimicrobialNucleotide
Syllabus - What you will learn from this course
1
Section
Module 1
Welcome and introduction to typing of bacteria and use of Whole genome sequencing applied to surveillance of bacterial pathogens and antimicrobial resistance
3 videos (Total 32 min), 1 quiz
3 videos
General Principles of typing of bacteria12m
Surveillance of Antimicrobial Resistance using whole genome sequencing12m
1 practice exercise
Module 120m
2
Section
Module 2
Introduction to Next Generation sequencing
3 videos (Total 37 min), 1 quiz
3 videos
Introduction to Next-Generation sequencing (NGS)19m
De novo assembly- from raw reads to contigs: assembler tool description and application5m
1 practice exercise
Module 230m
3
Section
Module 3
Whole genome sequencing tools- demonstration of analysis tools for species identification, MLST typing and finding resistance genes
3 videos (Total 30 min), 1 quiz
3 videos
MLST Typing: MLST tool description and applications8m
Resistance gene detection: Resfinder tool description and applications12m
1 practice exercise
Module 320m
4
Section
Module 4
Whole genome sequencing tools- demonstration of analysis tools for Serotyping of Salmonella and Escherichia coli strains , and finding plasmid replicons
3 videos (Total 24 min), 1 quiz
3 videos
E. coli serotype identification: serotype finder tool description and applications6m
Plasmid replicon identification and plasmid typing12m
1 practice exercise
Module 420m
4.6
50%
83%
29%
Top Reviews
By PT•Sep 17th 2017
Thank you great team from DTU, I get to understand NGS via your detailed explanation and useful demonstration as well as example exercise. Cheers
By VL•Jan 14th 2018
This is a very interesting course, it's practical and simple to follow and I've learned a lot about whole genome sequencing and its techniques.
Instructors
Lina Cavaco
Ext ResearcherCopenhagen University- ICMM /Statens Serum Institut - Department for Bacteria, Parasites and Fungi
Pimlapas Leekitcharoenphon
PostDocResearch Group for Genomic Epidemiology, DTU Food
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
When will I have access to the lectures and assignments?
Once you enroll for a Certificate, you’ll have access to all videos, quizzes, and programming assignments (if applicable). Peer review assignments can only be submitted and reviewed once your session has begun. If you choose to explore the course without purchasing, you may not be able to access certain assignments.
What will I get if I purchase the Certificate?
When you purchase a Certificate you get access to all course materials, including graded assignments. Upon completing the course, your electronic Certificate will be added to your Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. If you only want to read and view the course content, you can audit the course for free.
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Is financial aid available?
More questions? Visit the Learner Help Center.
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