Course: Eukaryotic Genome Assembly: How to Use BlobToolKit for Quality Assessment

In this screencast video you can see how sorting the table lets you explore datasets that have high levels on contamination. Click on the column ‘Hits matching target (%)’ to …

Let’s take a look at the genome assembly of Lucilia cuprina, the Australian sheep blowfly, which infects sheep with a disease called “sheep strike” or “flystrike” BTK plot for Lucilia …

The Tree of Life (TOL) programme at the Wellcome Sanger Institute uses the BTK pipeline and viewer as part of its genome assembly workflow. Contaminants and cobionts (Cobiont: Any organism …

The video here shows you how to use the Settings menu to change the shape of the plots, how to change the axes to zoom into a particular region, and …

In this video, Sujai explains how to use the Filters menu and the Tables view to display more detailed information about the different taxonomic groups that may be present in …

The BlobToolKit web viewer allows you to make lots of different changes to the display, helping you to analyse the plots and focus on the information most useful to you. …

In this video, Sujai explains the different views of the data you can access from the views submenu. You will learn more about some of these views later in the …

The BTK web interface might look confusing when you first start using it. There are many menu options on the top, and many filters that you can switch on and …

This week you have learned how to use the BlobToolKit webviewer. You should be able to use the menus to change the settings and look at different types of display, …

Square bins When you first open any genome assembly in the BTK viewer, you should see a blob plot that looks like this However, sometimes you see a plot with …

In this step you’ll look at the datasets for all birds with public assembly data available. To start, go to the BTK viewer and click on the “Datasets” top menu …

Where did the BTK viewer plots and analyses come from? The BTK web viewer is only a viewer. Behind the scenes, the BTK pipeline retrieves each genome assembly and the …

So far, you have seen how BTK can be used to explore individual genome assemblies. Sometimes it is necessary to look at many genome assemblies at the same time to …

Until now you’ve looked at all the different parts of the BlobToolKit viewer separately You have learnt about how the Settings, Filters, and the Datasets menus can be used to …

We have created a BTK handbook to help you install the pipeline and run it locally on your own assembly. It can be downloaded as a PDF here. This handbook …