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Voltar para Whole genome sequencing of bacterial genomes - tools and applications

Comentários e feedback de alunos de Whole genome sequencing of bacterial genomes - tools and applications da instituição Universidade Técnica da Dinamarca (DTU)

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1,178 classificações

Sobre o curso

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...

Melhores avaliações

AP

19 de jul de 2020

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.

MB

9 de jun de 2019

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.

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301 — 320 de 320 Avaliações para o Whole genome sequencing of bacterial genomes - tools and applications

por Bikash K

15 de jan de 2019

Very simple and informative

por Romain M

22 de jul de 2018

Great course, thanks

por Olga S

24 de jan de 2021

very practical!

por 121922201008 g

18 de set de 2020

Great

por Muhammad S A

16 de jan de 2022

5

por Deleted A

18 de jan de 2021

I found this to be a very well-structured course which gave me a good overview of a wide variety of tools used in the field. Among other things, I learned how to look for resistance genes and plasmids, and how to determine the species and sequence type of a sample. A sincere thank you goes to all those involved in putting this together.

Each weekly set of lectures is followed by a quiz, but perhaps a few more exercises would have been helpful... something on the lines of the final assignment (an exercise to learn how to interpret phylogenetic trees, for instance). What I think would also have helped is a brief description given by the lecturers of the biological features they were going to talk about - for example, what is the biological meaning of 'sequence type' of a strain? I think this would have made things clearer for beginners.

por Ioanna P

14 de abr de 2020

Interesting topic! And well presented material! It is very convenient and helpful to be introduced into several bioinformatic tools, as they may seem intimidating in the beginning. Also, I liked the final assignment.

I would suggest to add more assignments during this 5 week course as it is hand-on work and thus it motivates students to learn more and get familiar with the tools. It would also be useful to put more emphasis into the applications f these tools and how widely they are used. It would also be useful to do some troubleshooting during the course, like how we should interpret the results when they are not so clear or what we could further do to acquire a more clear picture.

Thank you very much for everything! It has been an enjoyable 5-week course.

por Jason B

27 de mar de 2020

There is very little background information given to what is being done, how it is being done or why it is being done. Obviously an online course like this can only go into so much detail but there was almost no explanation of the background. It is also not just using the medical field as its context but what is taught has almost no relevance outside medicine as the course is better understood as a tutorial on how to use their own web tools. While those tools serve their purpose, unless you want to use their tools, you will gain very little over the course.

por Arina D

1 de jul de 2020

This is a set of manuals. No theory - just a description of several tools with some very basic explanation of the principles underlying these tools.

Before applying for this course, I can suggest visiting the site with all the tools described in these courses and reviewing it - it may be easier for someone (and definitely faster) to read the instructions on the site https://cge.cbs. dtu.dk/services/

However, the tools themselves are quite useful.

por Lynn M

18 de set de 2020

Was slightly disappointed about how the class is very on the surface. It covers some cool tools but does not go into the details of genome sequencing, which I was expecting to see more of. Some lectures are highly repetitive as well.

por Lydia S

26 de abr de 2020

Got only rudimental knowledge of WGS but more detailed information how to use their pipelines- seems like a more commerical course than learning element.

I'd like the other course about antimicrobial resistance much better.

por Frédéric B G

11 de nov de 2019

This course has been mainly constructed to explain how the full set of bioinformatic tools developed by the CGE of DTU can be used. Personally, I would have preferred a course with more theoretical basis.

por James P

12 de ago de 2020

I thought this would be informative but the entire course is basically an infomercial for using their web based tools. Which to some, could be helpful but any serious bioinformatician should avoid.

por Luisa F D B

22 de jun de 2020

I liked some of the sections but the course is really focused on the platform developed by its university, so despite it is useful it does not give examples of another tool like BLAST

por Victor B C B

5 de ago de 2021

Poderiam explicar mais a fundo algumas definições e me pareceu que algumas ferramentas estão desatualizadas (Ex: Ferramenta para montagem, Velvet, a mais usada no momento é a Spades)

por Franziska N

1 de out de 2020

Good lectures, but unfortunately there is little general background transferred through this course. The lectures and the quiz seem mainly to be advertisement for their tools.

por Harvey T

29 de out de 2019

the presentation skills and the language were not so high. some files that need analysis are not working. But it is useful course by the end.Thx alot

por Sreedhar K

31 de jul de 2022

The explanation was not detailoed enough. exccpet for Shinny.

por Jing C

14 de nov de 2017

Wish it was more concise.

por Luka G

5 de jun de 2020

The course itself is great, unfortunately the person who designed it and is the main speaker has incomprehensible English, to a point that one needs triple the exertion to understand her. The transcript of the speech seems to be automatically generated, so one can not even read the lecture to understand it.