[MUSIC] Hello, everyone. Welcome to our course on Whole Genome Sequencing of Bacterial Genomes- Tools and Applications. My name is Pimlapas Leekitcharoenphon, or you can call me Shinny. >> And my name is Lina Cavaco. And I'm still here in this course. >> I am going to be the main instructor of this course. I'm a postdoc at Research Group for Genomic Epidemiology at National Food Institute at Technical University of Denmark. Not only me in this course. We also have additional teachers that involved in this course, Lina, Rene, Rolf, and Valeria. >> So besides this online course and previous courses that we have launched online, we also do research. And we have, for example, the of antimicrobial resistance. We do a lot of counseling nationally, but also internationally. And thereby we have EU Reference Laboratory for Antimicrobial Resistance. That is led by the European Commission, and we are the collaborating center for the World Health Organization, also in antimicrobial resistance. As part of our research, we have several projects focused on sequencing and use of whole genome sequencing. And the main ones we would like also to include here as part of the links that you can look up some data in. It would be the COMPARE project and the ENGAGE project. So, as part of this course, you will have the opportunity to go through five modules, and these modules will give you an insight to whole genome sequencing. And of course we should start with the introduction and give you an idea why and how we do bacterial subtyping and how we can introduce whole genome sequencing. Then we actually go to a second module where we introduce to the concepts and the theory behind whole genome sequencing and next-generation sequencing techniques. And we also introduce on how to can apply this. Then we have a few of the modules that go ahead there from with demonstration of some analysis tools where you can use the data obtained from sequencing and when you can use these tools that are online and freely available. And we have demonstrations for you to try out as well yourselves. And that would be several details. Shinny will go into more detail in these modules. But modules C and D and also E would be focusing on these demonstrations and tools. In the end, after the module E where you have already learned to use the tools and to also combine your data into phylogenetic trees, we will have a summative tutorial, which brings everything together and where you can try to be a detective and look up for your data and find out what are the outbreak strains in this. In each lecture of these modules, each module has several lectures, you'll be kept awake because you'll have questions inside the lecture. We have in-video quizzes, and you have graded quizzes at end of each module. As I mentioned, also at the end of the last module, there is an exercise that is more broad. And you will have a grading resulting from all these quizzes in the end. >> And after you completed this course, you will able to, first of all, you will know the concept and understand the principle of bacterial typing. And you will see different kind of applications of using whole genome sequencing for bacterial typing. And you will know why we will need whole genome sequencing for typing and what is the advantage of using whole genome sequencing for typing. And of course in the whole genome sequencing, you will know the basic and the concept of how do you sequence bacteria genomes using next-generation sequencing. And you will be able to know how to actually process the data, the raw data that you will get from sequencer. How can you know the query if it's good or not? How can you process from original raw reads data to something called assemble genomes or we can call contigs? And you will be able to manage once you get the contigs how can your typing, based on the sequencing data from the contigs, you will be able to identify species from doing sequencing data. You will be able to know the ST type or sequence type of your strengths. And you will know if your strengths contain any resistance genes and if your strains are E.coli or salmonella. You would be able to serotype them. And all the tools are the web-based tool that we have, and you will use for all kind of typing. There are individual tool, and you have to do submission individually, one by one, and we also have another tool called bacterial analysis pipeline that you will be able to submit all of your sample at the same time. For example, you have 10, 20, even hundreds bacterial trends at the same time. You put them, and you will get the answer or result at the same time and you will be able to use this tool. And if your bacterial trends, they are related or they are an outbreak or they are clone or not, so if you want to know if how do they related, how they part of the outbreak or if they're part of the colonial, you will be able to do it by constructing dendrogram or what we call phylogenetic tree based on SNPs or single-nucleotide polymorphism. And more importantly, you will be able to interpret whole genome sequencing results that we get from all the tool, not only our tool, but different tools, if you know how to actually make sense of the results and answer your question based on your results or study. >> So, having all these detail on what the course is about, you might be a little scared about how much knowledge you need to have in advance. And really, don't be. It is a course that is intended to be basic. So we will guide you through the basic knowledge that is needed to go further and to understand what the course and the whole genome sequencing analysis is about. Also, there is no need to buy any extra materials. Everything that you need is either in the lectures or added in as additional files into the course or links. And we recommend also to get to know also the people that are together with you in the course, and for that, we will have the discussion forums where we hope you participate, participate both in questions or bringing up interesting subjects. And we as teachers will be also part of these discussion forms. So we hope that you will enjoy and you'll have good use of this course. >> Yes. Thank you. >> Thank you. [MUSIC]