The datasets table view

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 sort it in ascending order (click again to sort in descending order). The genome assemblies with low “Hits matching target (%)” indicating high levels of contamination, include the species Pionus senilis, Psitteuteles goldiei, and Tichodroma muraria. All three have clearly separate proteobacteria blobs, which are common contaminants.

If you already expect some extra organisms in the assembly (e.g. Apicomplexan parasites from the tinamou bird genome discussed in Mark’s introductory video in Week 1) you can search for them specifically. Below the Datasets table, click on Customise Table. In the section Assembly statistics, click on the taxon drop down, choose Apicomplexa, and then choose Span and then click add. That will give you an additional column of the total span of sequences marked Apicomplexa. You can now click on this new column header and sort by that.

To avoid searching through large tables on your browser, you can click the “csv” button on the bottom right of the table, and export the data where you can explore/filter it in a spreadsheet.

The main thing to remember in this activity is that you can search through many public genome assemblies at the same time and compare their quality and the presence of non-target organisms like contaminants and cobionts.