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
Honorinacompleted this course, spending 12 hours a week on it and found the course difficulty to be hard.
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 distinction of displaying positive rapport to their aspiring students to learn creatively. Such honor and lauded appreciation goes to this team of Denmark Technological University---your CGE- Center for Genomics Study is such a valuable gift to aspiring clinical microbiologist researchers. you have given such clarity of vision and progressive motion…
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 distinction of displaying positive rapport to their aspiring students to learn creatively. Such honor and lauded appreciation goes to this team of Denmark Technological University---your CGE- Center for Genomics Study is such a valuable gift to aspiring clinical microbiologist researchers. 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. You are such great research scientists of this millennium.
All professors in DTU are so kind and their way of pdf presentations , quizzes and platforms of explanations to have a very impacting virtual classroom is so interactive.
Please add more courses, as all our colleagues are motivated with your such powerful determination to educate your learners of difficult things, yet they become easier as we ponder them all from the start to the end, reviewing what we had learned and applying them to the future endeavors in our careers in Clinical Laboratories.
This course is a pivotal joint to a brighter perspective of where are we all heading to----former days of PCR traditional genetics knowledge -unsystematized, complex and vague----but now becoming clear, simple and truly applied and reliably accurate accrued database of metagenomics. Someday, these learners will also contribute when they have the opportunities to further on in their studies. DTU---I salute you as my virtual Alma Mater. I sincerely thank you, whenever I become a future educator and academician in Manila, this knowledge given will be much of avail, God Bless
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!
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.
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.
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.
I am MS bioinformatics student, i complete two course on coursera, whole genome sequence and AMR. Thank You so much Mam for these courses. I learn a lot form these two courses so Mam please upload more course like this or make youtube channal and upload material related to Molecular Microbiology, it will be very helping for all.
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!!
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.
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.
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
i saw the course objectives and i feel in love with it. i got myself enrolled and i will loved it. The lecturers really knew their stuff and the class was very helpful. i have really acquired a lot after enrolling. 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. The online tools available through the Centre for Genomic Epidemiology were described thoroughly.
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.