DTU Denmark - Whole genome sequencing of bacterial genomes - tools and applications
- Offered byCoursera
- Public/Government Institute
Whole genome sequencing of bacterial genomes - tools and applications at Coursera Overview
Duration | 7 hours |
Total fee | Free |
Mode of learning | Online |
Difficulty level | Beginner |
Official Website | Explore Free Course  |
Credential | Certificate |
- Overview
- Highlights
- Course Details
- Curriculum
Whole genome sequencing of bacterial genomes - tools and applications at Coursera Highlights
- Shareable Certificate Earn a Certificate upon completion
- 100% online Start instantly and learn at your own schedule.
- Flexible deadlines Reset deadlines in accordance to your schedule.
- Beginner Level
- Approx. 7 hours to complete
- English Subtitles: Arabic, French, Portuguese (European), Italian, Vietnamese, German, Russian, English, Spanish
Whole genome sequencing of bacterial genomes - tools and applications at Coursera Course details
- 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
Whole genome sequencing of bacterial genomes - tools and applications at Coursera Curriculum
Module 1
Welcome lecture
General Principles of typing of bacteria
Surveillance of Antimicrobial Resistance using whole genome sequencing
Module 1
Module 2
Application of Genomic tools- One technology takes it all
Introduction to Next-Generation sequencing (NGS)
De novo assembly- from raw reads to contigs: assembler tool description and application
Module 2
Module 3
Species identification: KmerFinder tool description and applications
MLST Typing: MLST tool description and applications
Resistance gene detection: Resfinder tool description and applications
Module 3
Module 4
Salmonella Serotype identification: SeqSero tool description and applications
E. coli serotype identification: serotype finder tool description and applications
Plasmid replicon identification and plasmid typing
Mobile Element Finder: A web-based tool for detection of Mobile Genetic Elements in assembled sequences
Module 4
Module 5
Bacterial analysis pipeline- batch upload
Phylogenetic relatedness: CSI Phylogeny tool description and applications
Evergreen Tree: A platform for identification of foodborne bacterial outbreaks
Multipurpose detection of genetic markers- My Db finder tool description and applications
Tutorial
Final Remarks and perspectives
Text with Link to files to be used in tutorial
Module 5
Tutorial final Quiz
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