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Summary statistics for multiple assemblies

This article explains how to compare the statistics for multiple datasets
© Wellcome Connecting Science

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 tab. In the search box, type “Aves”, the class taxon name for all birds. You should see a table like the figure below.

screenshot for the previous link

The table shows all genome assemblies available in BTK viewer for Birds. The columns give you information about the species and assembly identifiers, some basic assembly metrics, which BUSCO lineage was most specific for that assembly, and how complete that BUSCO lineage was.

The last column includes the number of read sets found linked to this assembly in the public databases. If there are 0 read sets, then you will not find a BTK plot with coverage on the Y-axis, because there is no way to calculate the sequencing depth without the read sets.

The text below the table suggests how to use this table:

  • Click headers to sort results
  • Click a row to view an assembly
  • Type in the box at the top of each column to filter assemblies
  • Click on Customise table – to add extra columns to look for non-target organisms

Go ahead and click on “Customise Table” and enable these columns:

  • Assembly statistics

GC%, AT% and N%

  • Taxonomy

Target taxon

  • Summary Statistics

Hits matching target (%) – If this number is less than 100%, that means some sequences in the assembly did not match the expected target organism. The expected target in this case is the phylum “Chordata” (which includes fish, birds, mammals, etc)

BTK view customisable table

In the next step you will see how to use and interpret this table to explore the presence of non Bird DNA in this long list of Bird genome assemblies

© Wellcome Connecting Science
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