Whole genome sequencing of bacterial genomes - tools and applications

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Opleiderscore: starstarstarstar_borderstar_border 6,3 Coursera (CC) heeft een gemiddelde beoordeling van 6,3 (uit 4 ervaringen)

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Beschrijving

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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 chara…

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When you enroll for courses through Coursera you get to choose for a paid plan or for a free plan

  • Free plan: No certicification and/or audit only. You will have access to all course materials except graded items.
  • Paid plan: Commit to earning a Certificate—it's a trusted, shareable way to showcase your new skills.

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

Who is this class for: This course is for you if you are interested in getting to know more about Whole genome sequencing applied to bacterial characterization and surveillance. We aim at having a broad scope and international reach in different sectors. So this course us for you whether you are an undergraduate or graduate student, a researcher, medical or veterinary related professional, technical staff or simply interested in the subject!

Created by:  Technical University of Denmark (DTU)
  • Taught by:  Lina Cavaco, Senior Researcher

    Research Group for Genomic Epidemiology, National Food Institute
  • Taught by:  Pimlapas Leekitcharoenphon, PostDoc

    Research Group for Genomic Epidemiology, DTU Food
Level Beginner Commitment This course will run over 5 weeks, 2-3 hours a week Language English How To Pass Pass all graded assignments to complete the course. User Ratings 4.4 stars Average User Rating 4.4See what learners said Coursework

Each course is like an interactive textbook, featuring pre-recorded videos, quizzes and projects.

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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.

Syllabus


WEEK 1


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 expand


  1. Video: Welcome lecture
  2. Video: General Principles of typing of bacteria
  3. Video: Surveillance of Antimicrobial Resistance using whole genome sequencing
  4. Discussion Prompt: You own thoughts on applications for WGS

Graded: Module 1

WEEK 2


Module 2
Introduction to Next Generation sequencing


3 videos expand


  1. Video: Application of Genomic tools- One technology takes it all
  2. Video: Introduction to Next-Generation sequencing (NGS)
  3. Video: De novo assembly- from raw reads to contigs: assembler tool description and application

Graded: Module 2

WEEK 3


Module 3
Whole genome sequencing tools- demonstration of analysis tools for species identification, MLST typing and finding resistance genes


3 videos expand


  1. Video: Species identification: KmerFinder tool description and applications
  2. Video: MLST Typing: MLST tool description and applications
  3. Video: Resistance gene detection: Resfinder tool description and applications

Graded: Module 3

WEEK 4


Module 4
Whole genome sequencing tools- demonstration of analysis tools for Serotyping of Salmonella and Escherichia coli strains , and finding plasmid replicons


3 videos expand


  1. Video: Salmonella Serotype identification: SeqSero tool description and applications
  2. Video: E. coli serotype identification: serotype finder tool description and applications
  3. Video: Plasmid replicon identification and plasmid typing

Graded: Module 4

WEEK 5


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


5 videos, 1 reading expand


  1. Video: Bacterial analysis pipeline- batch upload
  2. Video: Phylogenetic relatedness: CSI Phylogeny tool description and applications
  3. Video: Multipurpose detection of genetic markers- My Db finder tool description and applications
  4. Video: Tutorial
  5. Reading: Text with Link to files to be used in tutorial
  6. Video: Final Remarks and perspectives

Graded: Module 5
Graded: Tutorial final Quiz

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