À propos de ce cours
4.6
172 notes
43 avis
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...
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Beginner Level

Niveau débutant

Clock

Approx. 10 hours to complete

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

English

Sous-titres : English...

Compétences que vous acquerrez

NucleotideAntimicrobialGenomeMicrobiology
Globe

Cours en ligne à 100 %

Commencez dès maintenant et apprenez aux horaires qui vous conviennent.
Calendar

Dates limites flexibles

Réinitialisez les dates limites selon votre disponibilité.
Beginner Level

Niveau débutant

Clock

Approx. 10 hours to complete

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

English

Sous-titres : English...

Programme du cours : ce que vous apprendrez dans ce cours

Week
1
Clock
1 heure pour terminer

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 vidéos (Total 32 min), 1 quiz
Video3 vidéos
General Principles of typing of bacteria12 min
Surveillance of Antimicrobial Resistance using whole genome sequencing12 min
Quiz1 exercice pour s'entraîner
Module 120 min
Week
2
Clock
1 heure pour terminer

Module 2

Introduction to Next Generation sequencing...
Reading
3 vidéos (Total 37 min), 1 quiz
Video3 vidéos
Introduction to Next-Generation sequencing (NGS)19 min
De novo assembly- from raw reads to contigs: assembler tool description and application5 min
Quiz1 exercice pour s'entraîner
Module 230 min
Week
3
Clock
1 heure pour terminer

Module 3

Whole genome sequencing tools- demonstration of analysis tools for species identification, MLST typing and finding resistance genes...
Reading
3 vidéos (Total 30 min), 1 quiz
Video3 vidéos
MLST Typing: MLST tool description and applications8 min
Resistance gene detection: Resfinder tool description and applications12 min
Quiz1 exercice pour s'entraîner
Module 320 min
Week
4
Clock
1 heure pour terminer

Module 4

Whole genome sequencing tools- demonstration of analysis tools for Serotyping of Salmonella and Escherichia coli strains , and finding plasmid replicons...
Reading
3 vidéos (Total 24 min), 1 quiz
Video3 vidéos
E. coli serotype identification: serotype finder tool description and applications6 min
Plasmid replicon identification and plasmid typing12 min
Quiz1 exercice pour s'entraîner
Module 420 min
4.6
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Briefcase

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a bénéficié d'un avantage concret dans sa carrière grâce à ce cours
Money

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a obtenu une augmentation de salaire ou une promotion

Meilleurs avis

par PTSep 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

par SKMay 18th 2018

The contents of the course were really very good and with loads of knowledge. Thank you very much for improving my knowledge in this area.

Enseignants

Lina Cavaco

Ext Researcher
Copenhagen University- ICMM /Statens Serum Institut - Department for Bacteria, Parasites and Fungi

Pimlapas Leekitcharoenphon

PostDoc
Research Group for Genomic Epidemiology, DTU Food

À propos de Technical University of Denmark (DTU)

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Foire Aux Questions

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