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Whole genome sequencing of bacterial genomes - tools and applications に戻る

デンマーク工科大学(Technical University of Denmark(DTU)) による Whole genome sequencing of bacterial genomes - tools and applications の受講者のレビューおよびフィードバック



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...




Thank you very much for this course through which i learnt basic handling of bioinformatics tools and concepts of WGS. This will help me a lot while pursuing my PhD research work in my field.



Excellent course with a wealth of information about tools and applications of whole genome sequencing. Presented in a very lucid and interesting manner, very crispy and simplified course.


Whole genome sequencing of bacterial genomes - tools and applications: 26 - 50 / 322 レビュー

by Arvind K


Very knowledgeable

by umashankar


Very nice content

by NG, S L


What I liked:

- Procedures for each tool are introduced clearly

- No off-topic lectures

- Each lecture's duration is appropriate

- The tutorial final quiz is helpful in consolidating our understanding of applying the tools

What needs to be improved:

- Describing the principles behind each tool (e.g. for CSI Phylogeny, I am only taught how to use it but I do not understand why SNPs are used for creating a phylogenetic graph).

- Some terms like "serology" and "SNP" are expected to be understood, so this is NOT a beginner's course as indicated (as of June 2022, these terms were also not explained in "Antimicrobial resistance - theory and methods").

- Would rather have a fullscreen presentation than videotaping the lecturer with the background because the words on the slides were too small. Could emulate Zoom playbacks where lecturers share fullscreens and have their talking heads on the right hand corner.

- For the tutorial final quiz video, it will be more challenging and more likened to real life if the lecturer doesn't tell us what tools to use and their functions (I guess this is why it is a beginner's course haha).

(- Less important but Shinny's accent is sometimes hard to decipher and the transcript translates wrongly but I do not blame her since she is not a native English speaker. Suggestion: find someone to fix the transcript for people who rely on visual learning (i.e. reading transcripts)?)


All in all, it definitely took some time for me to digest the applications and procedures for each tool. Luckily, when I really used them, they appeared to be user-friendly, so even if I forgot some steps mentioned in the lectures, I could deduce from the itembars.

Thank you to all lecturers for your knowledge!

by Catherine M


Can not even pass the first quiz, even with correct answers. The two videos based off the questions don't answer some of the questions if at all, and a google search or more in depth search revealed the correct answers, however the quiz continued to be incorrect no matter what correct answers you gave it.

by Piotr


W​eek 1 videos just throw a bunch of acronyms, without explaining anything, not even in depth, but in their relevance for the topic of the course. Similiarly, later weeks continously bring more terms with little explanation of them and providing little logic how are they connected to each other. Quizes don't relate to informations from vidoes anyhow or do so only in some of questions. Quizes don't provide any feedback.

by Gail C


T​he assignments are very difficult and I dont think the lectures provide enough information to do the assignments. Dont recommend this course.

by Aedrian A


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.

by razieh e


this course was very interesting and provide researchers with the most advanced tools to research into various topics like antibiotic resistance, virulence factors and etc. as i am really interested in antibiotic resistance, it gave me alot of useful information. i appreciate DTU and people who were in charge of teaching for this course. i really appreciate MS Pimlapas Leekitcharoenphon because she was a skilled person in this regard and her teaching method was very good.

by Adewole A


I found the delivery of the course content quite interesting and the topics covered were perfectly explained to give both theoretical understanding and hands-on skills. The range of applications and tools covered on the DTU website will definitely be invaluable in carrying out detailed analysis of my sequence data. T​hank you so much for the wonderful course and I would highly recommend it to anyone interested in bacterial WGS.

by Audrey V


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 Kristine L C


Thank you to the entire DTU team that made this course. It's a very informative course with hands-on work using CGE tools developed. Glad that some aspects of the course are related to my line of study and this brought me even more knowledge to my passion in microbiology. Hoping for more courses from you soon! Thank you very much!

by Tahmina B


This course is very useful for bacterial genome analysis in respect of very technical and specialized identification of the resistant genes . I have learnt different skills from this course which will help my future research work in a large scale. Thanks to DTU team and Coursera team for this valuable course.

by Grigore-Mihaita S


It was a nice experience which i kindly recommend to everyone who is interested in improving their knowledge in microbial genomics, learning to use bioinformatics tools provided by the Center for Genomic Epidemiology but also to interpret the resulting data. Thank you for this amazing experience!

by AKM F H


This is a really good course for beginners as it explained the use of some fantastic web-based tools to detect bacterial ST, resistance, plasmid, MLST, and phylogeny. I have learned a lot of new techniques to analyze the whole genome of a bacterium. Thank you for giving me the opportunity.

by Sebin J


It was a great course which introduced me into the world of whole genome sequencing and application of various tools for finding bacterial sub-typing, serotyping of plasmids and constructing phylogenetics trees. Really satisfied with course and looking forward to more courses like this.

by Amro H


Thank you for the very helpful informative course. Very useful online tools. and great effort.

Only may we try to improve the English subtitles and attach answer for the quiz even at the end of the course?

Thank you again for all of your help, you are doing an OUTSTANDING job.



The course was very much helpful for my current work and it helped me understand many things especially on data analysis front of whole genome sequencing of bacteria. I would like to thank all the tutors of the course for giving their time for the development of this course.

by Mohamed E 2


Not to mention, the power of the tools illustrated in this course, I just wanna mention that I am senior student in bioinformatics bachelor degree and Dr. Pimlapas Leekitcharoenphon is by far the best instructor I have ever come across in the field till now. Thank you.

by Orlando R


Congratulations to the team preparing and delivering the course it is very well designed, organized, and delivered, the presentations are clear, the quizzes are very helpful, the tools are excellent, in summary, a very good course, thank you very much to all of you.

by Opeyemi U L


The module was easy to follow and the class exercises made it very easy to understand. I will highly recommend this course to microbiology students especially the ones without prior knowledge of basic bioinformatics for epidemiological study of bacterial infections

by Katya B H V


I highly recommend this course, even for me a non molecular biologist/medical student, it was very helpful and very enriching. I am so grateful to all the professors for sharing their experience with us. I will keep an eye on the future courses of the DTU.

by Joseph A M I


Very thorough course about WGS. They did a good job explaining from the beginning for those like myself that have very little experience. From there, they taught us how to use their web-based tools and even gave us little assignments to test our knowledge.

by Napakhwan I


This course provides one of the simplest ways to become familiar with whole genome analysis and its applications. As I am the one who is trying to understand NGS and WGS things, I would say this course is absolutely helpful. Thank you all instructors.

by Nimat U


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 Sadia N M


It has been an wonderful journey. The instructors clearly explained the topics and the course materials were helpful to grasp the topics they were teaching. Highly recommend this to anyone who is keen to learn about bioinformatic tools in simple ways.