Square bins, missing plots, and cumulative plots

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 square bins rather than circles:

The reason is that in some genome assemblies there are hundreds of thousands of small contigs, and displaying them as individual interactive objects can slow down or even crash the web browser. By default, BTK viewer shows these assemblies as “binned” blob plots – with individual bins in the shape of squares. The binned blob plot is a very powerful tool for examining large numbers of contigs interactively. In fact, one of the main innovations of the BTK viewer is the ability to visualise thousands of separate taxonomic assignments interactively using these binned plots. You can use the Settings main menu to change the plot shape back to a circle, as you saw in the screencast video in step 2.6.

Missing Blob Plots and cumulative plots

In many cases, such as the figure below, there is no read data directly linked with the genome assembly in the public databases. In these cases, the BTK pipeline is unable to automatically calculate the sequencing depth and show that on the Y axis. If you are a researcher with a genome assembly like this, please contact blobtoolkit@genomehubs.org with the publicly available read accession numbers for a given genome assembly and the pipeline will be rerun for that genome.

In cases like this, where BTK has not yet calculated sequencing depth, the default view is the “Cumulative” plot, which shows the number of contigs in the assembly on the X axis (ordered from longest to shortest), and the cumulative length of the genome assembly for those contigs on the Y axis.

In this plot for the milkfish Chanos chanos, the cumulative length plot rises sharply for the first 16 contigs, reaching a genome span of just over 650 Million bases, and the remaining 14 sequences (from number 17 to 30) in the assembly are very short, so the cumulative length plot is almost flat.