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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. 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

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Rating 4.5 based on 211 ratings
Length 6 weeks
Effort This course will run over 5 weeks, 2-3 hours a week
Starts Jul 17 (41 weeks ago)
Cost $49
From Technical University of Denmark (DTU) via Coursera
Instructors Lina Cavaco, Pimlapas Leekitcharoenphon
Download Videos On all desktop and mobile devices
Language English
Subjects Science
Tags Life Sciences Clinical Science Animals And Veterinary Science Research

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What people are saying

whole genome sequencing

Whole genome sequencing is a wide area of science that combines knowledge in Biology, Computer Science and Mathematics.

This is an excellent course to get started on the topic of whole genome sequencing.

This course enabled the learner to get novel insights into the application of whole genome sequencing of bacterial genomes, demonstrated the analysis tools/pipline available online for multiple analyzes.

When I started this online course, I had loophole in how I should handle my sequences for whole genome sequencing.

But now, I'm grasp the full understanding behind whole genome sequencing and have changed my project outline since then.

i must confess, i will recommend the course for any student wanting to learn Whole Genome Sequencing Excellent introductory course - understanding the theory and application of the knowledge were both covered.

I will highly recommend this course to microbiology students especially the ones without prior knowledge of basic bioinformatics for epidemiological study of bacterial infections 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.

pMLST of question 9 Quiz 4 GOOD ONE TO GET KNOWLEDGE ABOUT WHOLE GENOME SEQUENCING AND BACTERIAL SUB TYPING Good course, with amazing hands-on practice.

I am sorry if "Discussion Forum" is already there and I have ignored that.Thanks You very much,Gourab Das This course provides a first hand view of whole genome sequencing (at the contig level anyway) as well as providing the concepts and tools for characterizing and typing bacteria and their associated plasmids.

It really shed light on many aspects on whole genome sequencing Course contains relevant application based material.

Very much enjoyed the course and the practice problems involving Whole Genome Sequencing on the CGE website 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 This course is mostly just an advertisement for the particular tools created by the CGE.

Generally, help me understand whole genome sequencing of bacteria.

Excellent course with a wealth of information about tools and applications of whole genome sequencing.

Thanks :) By taking this course, I am able to advance my knowledge on whole genome sequencing of bacterial genomes and this course explores the applications of different tools for identification of bacterial species and its sub types.

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very useful

Very useful course.

Very useful and enjoyable!!

Learnt a lot very useful.

It was very interesting to try upload genome and use various tools for identification of the pathogens and resistance mechanisms.Very useful information and excellent excercises.

Very useful and helpful course to know how to interprete your results in different platforms and tools.

It was motivating and very useful!

Very useful online tools.

Its an awesome and very helpful course This course was very useful and simple to learn and understand.

I really enjoyed doing the course and hope tit will help me in the future i had finally learned it really helpful and awesome course Very useful course but it will be great if tools are explained in little more detail.

very useful ,thank you so much !!

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easy to understand

The module was easy to follow and the class exercises made it very easy to understand.

It's an amazing, well-organized course, easy to understand and apply.

Nice good Excellent course with easy to understand explanation and illustration from the instructors.

they literally made it very easy to understand the process and the manner of how to execute them.

This was very informative and easy to understand course for beginners.

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so much

Thank you so much for the professors as they shared the knowledge and experience with me.

Thank You so much Mam for these courses.

Cheers Excellent, had so much fun doing the course.

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.

It is a very wonderful and informative lecture & thank you so much Coursera & DTU for your amazing presentations.

Thank you so much for such effort.

Obviously an online course like this can only go into so much detail but there was almost no explanation of the background.

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very interesting

The tools mentioned are very easy to use and applications of the tools in the real world is very interesting.

It is a very interesting course and I recommend it.

The tools provided are very interesting and easy to use Es un curso bastante fácil para entender las herramientas bioinformáticas que tenemos actualmente para interpretar el genoma bacteriano.

A very interesting course.

That was really awesome.Thanks to everyone It has very hard but very interesting for my career I am a biology student, who recently started a masters in bioinformatics and have been struggling to try to keep up with the computational aspects and this course was perfect for me.

The topics of the course are very interesting and well curated.

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bioinformatic tools

Such a good course which gives an overview to some of the bioinformatic tools that can be employed in genome sequencing.

This course has been mainly constructed to explain how the full set of bioinformatic tools developed by the CGE of DTU can be used.

Thank you very informative, learn't new bioinformatic tools, Precise, crystal clear and fun learning sessions.

It is very convenient and helpful to be introduced into several bioinformatic tools, as they may seem intimidating in the beginning.

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well as

Thank you great team from DTU, I get to understand NGS via your detailed explanation and useful demonstration as well as example exercise.

you have given such clarity of vision and progressive motion of what is the future of Medical Pathology Diagnostics and all supplanted fields of Microbiology and Genomics, as well as Metagenomics.

It gives both theoretical as well as practical knowledge of Whole Genome Sequencing.

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Careers

An overview of related careers and their average salaries in the US. Bars indicate income percentile.

GS Whole Loan Portfolio Closer/Analyst $48k

PhD, Clinical Genome Analyst $69k

Whole Body Buyer $71k

Global Marketing Manager, Whole Blood Automation $99k

Scientist, CRISPR/Cas9 Genome Engineering $114k

Scientist – Genome Analysis Unit (Computational Biology) $116k

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Rating 4.5 based on 211 ratings
Length 6 weeks
Effort This course will run over 5 weeks, 2-3 hours a week
Starts Jul 17 (41 weeks ago)
Cost $49
From Technical University of Denmark (DTU) via Coursera
Instructors Lina Cavaco, Pimlapas Leekitcharoenphon
Download Videos On all desktop and mobile devices
Language English
Subjects Science
Tags Life Sciences Clinical Science Animals And Veterinary Science Research

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