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Summary of assessing a public assembly

public assembly

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 see which public genome assemblies have non-target organisms such as contaminants, or parasites, or other cobionts.

In this section we have put all the steps together in one place in text form, rather than video, so you can refer to them whenever you want to check a genome assembly in the BTK viewer.

Steps

  1. Go to BTK viewer
  2. Use the search bar or the tree view to find your species or higher level taxon of interest (eg Mammalia, or Aves) and select a species to view
  3. Only species with 1 or more in the Read-sets column will have blob plots. Click on the row or species name
  4. If the blob plot is binned, use Top menu > Settings > shape > circle, to view a more traditional circle plot
  5. If the blob plot is static (because it has too many sequences), use Top menu > Settings > interactive
  6. Can you see clear and separate blobs? If not, you might have to zoom in to the plot (use Settings > x-axis range and y-axis range to change the ranges)
  7. Use Filters > length, to see only the long contigs, or only the short contigs at first
  8. Use Filters > gc, to remove any blobs with very high (or very low) GC content
  9. Use Filters > READACCESSION_cov
  10. If there is more than one READACCESSION_cov, use the side buttons to plot one on the x-axis, and one on the y-axis. Any contigs far from the diagonal, with zero or low coverage in one read set, are likely to be cobionts as they do not have the same relative coverage in both read sets
  11. Use Filters > TAXRULE_TAXONLEVEL with different taxon levels such as Phylum, Order, Family, etc to see if different species clearly belong to different blobs?
  12. Use the view submenu “table” to see a list of all visible contigs, and sort by length/coverage. Click on the coloured boxes to see if the blast hits are consistent across the whole sequence
© Wellcome Connecting Science
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Eukaryotic Genome Assembly: How to Use BlobToolKit for Quality Assessment

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