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Whole genome sequencing of bacterial genomes - tools and applications

Technical University of Denmark (DTU) via Coursera


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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


  • Module 1
    • Welcome and introduction to typing of bacteria and use of Whole genome sequencing applied to surveillance of bacterial pathogens and antimicrobial resistance
  • Module 2
    • Introduction to Next Generation sequencing
  • Module 3
    • Whole genome sequencing tools- demonstration of analysis tools for species identification, MLST typing and finding resistance genes
  • Module 4
    • Whole genome sequencing tools- demonstration of analysis tools for Serotyping of Salmonella and Escherichia coli strains , and finding plasmid replicons
  • Module 5
    • Whole genome sequencing tools- demonstration of analysis tools for multiple analyzes, phylogenetic tree building and finding genetic markers from self-made databases and Summative Tutorial exercise

Taught by

Lina Cavaco and Pimlapas Leekitcharoenphon


4.8 rating, based on 20 Class Central reviews

4.6 rating at Coursera based on 1439 ratings

Start your review of Whole genome sequencing of bacterial genomes - tools and applications

  • Honorina Magno Nuguid
    Though it is really hard at the end quiz, the most interactive quiz I have ever had in MOOC, yet the Instructor, Ms. Pimplas is so motivating proctor in every way. I nominate DTU as the best Biological science Education provider. It gives a certain…
  • This is an excellent course, both in itself and as a state-of-the-art follow-up to the DTU's "Antimicrobial resistance - theory and methods" course. This offering truly presents the expertise and the achievements of DTU in the field. The graded activities are interactive and a good review of principles in bioinformatics, using the homegrown free-to-use resources by the institution. Conventional routine microbiologists and academic scientists working in the field should own the relevant skills to generate and handle molecular microbiological data, and this course is a good place to start.
  • Anonymous
    We offer a hands-on training on WGS, however, the data analysis portion is lacking. Prior to taking this course, I believed that only bioinformaticists could interpret NGS data as it was so foreign to me as an analyst and I would have to learn Linux command line in order to interpret my results. I was wrong, I learned a lot from this course. The lectures were very clear and I even enjoyed the quizzes. It added a practical element to what we were learning, especially the last case study. I now use the CGE online software and we even include a demo in our hands-on training to help those from smaller organizations who do not have the budget to hire dedicated bioinformaticists. Thanks DTU, WGS instructors!
  • Anonymous
    The course is one of the best courses I have ever taken on Coursera. Whole genome sequencing is a wide area of science that combines knowledge in Biology, Computer Science and Mathematics. This course Whole Genome of Bacterial Genomes: Tools and Applications is straight to the point and very good for microbiologist and anyone who is interested in studying genomes of microbial pathogens not just bacteria. I recommend every microbiologist working with pathogens take this course to enlighten, broaden and improve their knowledge in genomics which is becoming integral part of almost every Biological studies.
  • Anonymous
    This is an amazing experience in understanding the nature and function of genome sequencing. The tools mentioned are very easy to use and applications of the tools in the real world is very interesting. I would recommend this course to students who are more interested in Genetics or Genome Sequencing and wants to apply for a job Informatics specialist or Genetics Specialist. I completed the course and got certified which enabled me to apply for different positions in different companies. Thank you so much for the professors as they shared the knowledge and experience with me.
  • Anonymous
    This is an excellent course to get started on the topic of whole genome sequencing. I am a water technologist recently involved in many projects on resistance.

    The course presents in a clear way the basic things you need to know to determine antibiotic resistance using sequencing. I really appreciate the introduction to the online tools with easy examples.

    I am simply very grateful for this course.

  • Profile image for Ignazio Sammarco
    Ignazio Sammarco
    Very useful course. After completing the course I had opportunity to work with Whole Genome Sequencing of isolate from Salmonella samples . The lessons helped me a lot to put into practice a Bioinformatics pipeline for Species identification applied to surveillance of bacterial pathogens and antimicrobial resistance gene detection for meat and human samples.
    Thanks to you all professors and I hope in the future to take another class with you.
  • Anonymous
    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. For example, surveillance of antimicrobial resistance, especially you can build your own database using My Db finder to detect genetic markers. Very useful and enjoyable!!
  • Pawan Parajuli
    This course was an excellent course. I was glad that I completed the course and obtained the course certificate. It taught me several tools to get insight of the bacterial sequence data and get the information about its annotation. Thank you the centre for genomic epidemiology, Technical University of Denmark for offering this course.
  • Anonymous
    I really enjoyed the course, it was a good introduction to WGS providing an overview of the many tools that DTU offers in this field. I would recommended to those with an interest in this new analytical method, no previous knowledge of WGS required.
  • Profile image for Nibir Parasar
    Nibir Parasar
    amazing as it allowed me to understand the basics to understand better than before.the tools are really handy during my own research.All the mentors's way of teaching is crisp and clear.
  • Anonymous
    It is such a practical, detailed and useful course for users. I learned a lot about how to tackle my next generation sequencing data through the study. It is really a fruitful journey. Come and join, guys.
  • Profile image for Gabriela Giacoboni
    Gabriela Giacoboni
    It is a very interesting course and I recommend it. I could not finish it in the stipulated time. I want to take it back when I have more time. congratulations to the team!
  • Profile image for Yun Wu
    Yun Wu
    It was a good introduction for web-based tools on bacterial genomics. For people who do not wish to learn hard-core command line tools, CGE provides a great alternative.
  • Anonymous
    The course material was very very useful for me. The content was detailed and it started step by step. I would like to join similar courses in the future.

  • Anonymous
    An amazing course, highly organized with an amazing hands-on material. I recommend students trying the bioinformatics field to take it
  • Anonymous
    it was very helpful and useful. will finish it and use my learnt skills for my analysis. absolutely lovely course and tutors.
  • Anonymous
    Thank you to the all team at CGE for making this course available to us. 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 would like to see how you develop can one handle metagenomics data using your web tools pipelines
    Thank you once again
  • Anonymous
    Excellent introductory course - understanding the theory and application of the knowledge were both covered. The online tools available through the Centre for Genomic Epidemiology were described thoroughly.
  • Anonymous
    A very interesting course, well designed specially for beginners which needs a strong background before going into more detail stuffs

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