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Back to Whole genome sequencing of bacterial genomes - tools and applications

Whole genome sequencing of bacterial genomes - tools and applications, Technical University of Denmark (DTU)

4.6
215 ratings
•
58 reviews

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...

Top reviews

By SK

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May 18, 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.

By SA

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Mar 12, 2018

one of the best courses ever i learned so many things in a short period. looking forward to your next course.\n\nThanks

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58 Reviews

By Adeyemi Samuel

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Feb 20, 2019

Please, improvements on the bioinformatic tools and the zipped files will be appreciated, i had little difficulty opening and accessing them on my andriod device, however overall, the course was enlightening

By Robert Furrow

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Jan 28, 2019

This course is mostly just an advertisement for the particular tools created by the CGE. It would have benefited from deeper explanations of the algorithms at many points. It didn't really build skills, though I am certainly more aware of the breadth of their online tools now.

By Lydia Mutanda

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Jan 24, 2019

Such a good course which gives an overview to some of the bioinformatic tools that can be employed in genome sequencing. I'm glad I enrolled for this course because it has enlightened me of the other part of molecular biology I didn't know so much about.

So thanks to all the instructors that dedicated their time to provide us with new knowledge.

By Bikash Karki

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Jan 15, 2019

Very simple and informative

By Ali Abdelkareem Ali Eisa

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Jan 08, 2019

applications

By Sören Wacker

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Jan 07, 2019

It is basically a commercial for their tools. Not much content to learn.

By Jana M

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Dec 15, 2018

Great course, but very challenging. You need to be advanced in biology to do this course.

By Kira Kondratieva

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Dec 04, 2018

This is a great class presenting a user-friendly web tool CGE pipeline that is ready to help all researches with their bioinformatics data. It can even build phylogenetic trees!

And I loved a small detective game at the end of the course when we needed to process unknown bacteria sequences to see if it was a real outbreak and what antibiotics were able to stop it!

A lot of thanks to the team!

By AGBO ACHIMI ABDUL Jabar B Pacome

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Nov 29, 2018

perfect course . very instructive and well detail

By WAI Kin Lung

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Nov 27, 2018

Great course that help student to understand the application for non computing scientist.

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