[MUSIC] Hello everyone. My name is Pimlapas Leekitcharoenphon. I'm a Postdoc from Research School for Genomic Epidemiology at DTU Food. Today, I'm going to be presenting you a bacterial analysis pipeline or batch upload. If you already use the tools from Center for Genomic Epidemiology, you can see that we have different type tools for you to use. And if you have only one sample, then that's easy. If you want to know how to type in results then you can submit your one sample into different tools that we have. Let's say you can submit to know in using. You can know the ST type by ST. You know specie by of. If you have one sample, it's fine, or two or three or five samples, it's fine. Then you can do submit your genome individually to each of the tools that you want to know the answer of the typing that you want to know. But let's imagine that if you have a 100 genomes, or even a 1000 genomes. It's not possible, or not practical, that you actually have to submit 100 submissions individually to know all the typings of your hundred samples. And that's why we made these bacterial analysis pipeline, or batch upload, for you, as you have the batch, or the bunch of unknown samples. And your unknown sample can be in raw reads. Or can be in assemble genomes or combination. So you put all of them into the same set of data and upload all of them to the tools batch upload. And the batch upload will give you all the typing results of all the uploaded genome that you submitted to the tool. So here is the web link to the tool and when you. The first time that you use the batch upload, it will show you this page. And you have to register as a new user. So you click new over here, and then you put your email, user name, password. And confirm password and put these numbers that you see over here. And then, you will get email and then you confirm the registering by clicking your email. And then once you already register you're going to see the same page again. But once you continue here you will see another page that is actually the web page for the batch upload. So it contains five steps that very easy. So the first step, you have to download metadata template. Of course, when you submit 100 genome. Or a number of genomes you'd have to submit metadata alongside with your genome. Furthermore, you have to download the template. It's just normal Excel. And then you fill out the template. Then you upload the template back to the tool. And then, you select the five, and you submit all the five together with the metadata. So, let's start by filling out the template. So, the template, as I told you, is just a normal Excel that has different columns. And if you don't know what to fill in in this column, you can go to attribute description. When you click here it's going to show you what you can fill in each column. And the column that they are mandatory is going to be in bold. Fairly intense black over here. Anything in bold, they are mandatory. They need to be filled. Otherwise the tool will not accept your metadata. So let's say the file name, yes, of course, is one of the mandatory columns. So you have to put the genome file that you want to upload to the tool. And remember the file names have to be exactly with the file name in your sample when you put it here. Otherwise, the tool cannot find your genome file. And then you have to say, is this pre-assemble or not? If your genomes is already assembled then you say yes. And if not, then you think no. If it [INAUDIBLE] then you have to say no. And then when it's [INAUDIBLE] and you say no, it's not pre-assembled, then you have to fill these two columns. Save in the platform. Illumine or Antonin or whatever sequencing platform that you use. And then sequencing type is a single pair made pair. If your samples are already assembled then you say yes. And then you don't need to fill anything over here about the sequencing platform or sequencing type. Another mandatory is country, that you have to put the country of your sample. And the isolation source, that also mandatory. And the isolation source is have only option for human, water, food, animal, laboratory, other, or unknown if you don't know. Another mandatory column is collecting date. In this case, you can put day, month, year. Month, year, or just only year. And here is an example of my metadata. So in this case my samples they are a simple genome. Then I can put only one genome in sample. And then because it's pre-assembled and I say yes. Because it pre-assemble when you say yes for pre-assemble, you don't need to fill sequencing platform or sequencing type. But if your genome is raw read then you have to say no for pre-assemble and you have to fill the platform of the type. And remember, your raw read can be single and a pair in. And a single end, you have only one file then you can put one file over here. But if your sample is pair and read, then you have two files. For example, the way that you put two file. You put the first file here and then you have one space, only one space, and you put another file. Therefore pair and reads. Now I finish the download template. These are the templates. The next step, you have to upload the template that you filled out. And if your template correctly filled out it's going to say in green over here that Excel template uploaded correctly. If you have some error or made some mistake in the metadata when you filled it in. It's going to show over here warning sign over here until your work is actually missing or error that the program found in your metadata. And once you have the metadata uploaded correctly, then you choose your genome files. All the genome files that you put in the Excel templates you put everything here, like this, in this case I have five genome. Now you are ready to submit all of your genomes together with the metadata to the server. So you click submit. And if, you're going to see the progressing bar in blue, like this. So when, until the end, that's mean it's done. And when it's done, it's going to show you the next page that is optional for you. If you want to put your email over here and click notify me via email. Meaning that when the program finished analyzing your genome, if you send you an email with the output link in the email. So I re-recommend you when you use batch upload because you normally put many genomes. And of course it going to take more time to finish out analysis. Especially if your genomes are raw read because the program has to know assembly of all of your sample before it starts to do any other analysis. So here is an example of the output that you will get from the batch upload. So you get our example over here. If you want to know more detail in all of your samples. You go to the sample manager where you click at the sample manager. It will show you again all the sample that you have over here. And you can have two options to actually get out of typing this out in an Excel sheet. So the first one, all the data in Excel sheet. And the second one, downloaded we see some data in a more detailed Excel format. So let's have a look at the first one, the first option of Excel. So this is the Excel output that you will get. Of course you get the Sample ID and all the information that you put in the metadata. And if you go further to the right. You see genome five. That's best on the assemble quality. And number of contigs. And 15, those three things are for quality control of the deno assembly. And of course, you have species, and you have the MST sequence type. And you have the detail of the alleles that you found in the MST tool. And of course you have [INAUDIBLE] and genes. And if you can have team's classmate and POST. So this Excel sheet we put all the resistance genes into the same column. But if you choose another Excel's over here, you will see more detail on the recessive gene. Because it divide, put the gene accordingly to the antibiotics. So you can see more detail of the recessive gene according to the antibiotics. And if you go back again to the sample and if you click over here you can see the detail of the tools that the program used to analyze your genome. And if you click each of the tools you can see more detail of the output from each of the tools here. And if you want to reanalyze your sample, you don't need to upload your sample again. If I want to reanalyze my frame number five then I click analyze. And then you can choose what you want to reanalyze, like sample. I want to do ResFinder again to identify receding genes. But I want to lower it down my percent identity, than you can do with the analysis over here. And if you see the end of the pairs for the best upload, you can see the technical problem. So if you have any problem using the tool, you click on Technical Problem and email us your problem. And thank you for very much for watching. [MUSIC]
