Explore

Whole genome sequencing of bacterial genomes - tools and applications

Approx. 7 hours to complete

Save Course

Go to Course

Course Summary

Explore the world of bacteria with this course that covers their biology, genetics, evolution, and interactions with the environment.

Key Learning Points

Gain a deep understanding of bacterial biology and genetics
Learn about the evolution of bacteria and their interactions with the environment
Explore the latest research in the field of bacterial science

Learning Outcomes

Understand the basic biology and genetics of bacteria
Recognize the importance of bacteria in the environment and their interactions with other living organisms
Evaluate the latest research in the field of bacterial science

Prerequisites or good to have knowledge before taking this course

Basic knowledge of biology
Access to internet and a computer

Course Difficulty Level

Intermediate

Course Format

Online
Self-paced

Similar Courses

Introduction to Microbiology
Genetics and Evolution

Related Education Paths

Related Books

Description

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

Outline

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

Summary of User Reviews

Discover the fascinating world of bacteria with this course on Women's and Gender Studies. Students have praised the engaging lectures and informative content that make complex topics easy to understand.

Key Aspect Users Liked About This Course

Engaging lectures and informative content

Pros from User Reviews

Well-structured and organized course
In-depth coverage of bacterial biology
Great supplementary materials and resources
Active and helpful community of learners

Cons from User Reviews

Some sections may be too technical for beginners
Limited interaction with course instructors
Not all topics may be applicable to all students

Recommended for you

Whole genome sequencing of bacterial genomes - tools and applications

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....

Save Course