Get to know the BlobToolKit Viewer by following these tutorials.
Public vs. local instances
We host a public instance of the Viewer at blobtoolkit.genomehubs.org/view where you can explore our analyses of thousands of publicly available datasets. If you want to use the Viewer on your own data then you will need to set up a local instance. Read more…
Searching available datasets
There are two ways to search for available datasets: (i) using the search box to search by dataset id or any term in the dataset metadata, e.g. phylum or assembly accession; or (ii) browsing the NCBI taxonomy to find datasets by taxonomic group in the public instance. Read more…
Exploring views
Each dataset is represented by several interactive plot types: blob, cumulative, snail and table. For datasets with read data that have been mapped to the assembly, the blob view is shown by default, otherwise the view defaults to cumulative view. All views update automatically based on changes to filters (see Filtering assemblies) and other settings (see Adjusting plot settings). Read more…
Changing plot axes
Blob plots show GC vs. coverage by default but can be adjusted to plot any available variable on either axis and to use alternative ranks (other than phylum) to set category colours using the Filters menu. Read more…
Adjusting plot settings
For each plot type, a number of settings can be adjusted, either to manipulate the plot to help explore specific features or to modify the appearance to generate a publication-ready image to export. Some of these settings are shared across plot types, while others are plot-specific. Read more…
Filtering assemblies
Assemblies can be filtered interactively by setting variable value ranges or selecting taxonomic categories in the Filters menu. Individual scaffolds or all scaffolds in specific bins can also be filtered based on selections. Read more…
Using selections
In addition to providing a mechanism for Filtering assemblies to extract or exclude features observed in blob plots, selections can be used to explore datasets by tracking specific scaffolds between views. Read more…
Reproducing interactive sessions
Most interactions with the Viewer automatically update the URL in your browser, allowing sessions to be saved, shared and restored by copying and pasting the URL from your browser’s address bar. Selections cannot be stored in the URL but can be exported and reloaded along with all other parameter settings using the Lists menu. Read more…
Viewing large datasets
The Viewer is designed to allow browser-based interactive exploration down to the individual scaffold level of preliminary and published datasets. For particularly fragmented assemblies, this can involve processing several million individual scaffolds so several options allow such assemblies to be displayed without losing responsiveness. Read more…
Hosting a local instance
To use the Viewer with locally generated BlobDir datasets, you will need to host a local instance of the Viewer. Convenience methods exist within BlobTools2 (see BlobTools 2 tutorial Opening a dataset in the Viewer) to start the Viewer with no additional configuration but more options are available when starting the Viewer directly. Read more…
More planned tutorials (coming soon…)
Making a local instance publicly accessible
Using the Application Programming Interface