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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
190 ratings
•
51 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 VL

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Jan 14, 2018

This is a very interesting course, it's practical and simple to follow and I've learned a lot about whole genome sequencing and its techniques.

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.

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51 Reviews

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.

By Audrey Vanya

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Nov 21, 2018

I only just begin taking part in it and all I can say is I am enjoying it even though I am a bit behind schedule and my first attempt was 60%, I will try again and aim high with better understanding. Thank you for the opportunity and the financial aid that was approved for me to attend the course. I am determined to do my best. What I also like is the clear teaching or lecturing manner of all the presenters of the course.

By Hamza Arshad Dar

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Nov 09, 2018

I like this course very much! The instructors were really helpful in getting their point across.

By Ahmed Elnemr Abo elez

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Oct 31, 2018

It isa fantastic course to spend your time

By Luis Eloy Homobono Fuentes

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Oct 28, 2018

It's a great course and it's not so difficult

By Nimat Ullah

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Oct 20, 2018

Thank you very much to all the team of DTU for organizing this course and made it easy for every student/researcher to analyze genomic sequence data. This course was very helpful to me and I appreciate Dr. Shinny for her excellent teaching methodology.

By Josue Daniel Carrasco Caceres

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Oct 03, 2018

Excelente curso, brinda una gran cantidad de herramientas muy útiles para realizar investigación.

By Sayan Poddar

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Oct 01, 2018

This course helped me a lot in determining bacterial typing. Just one question, in some quizzes I got some answers wrong so is there any way of knowing the right answer.

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