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Working with multiple data sets

multiple data sets
So far, you have seen how BTK can be used to explore individual genome assemblies.

Sometimes it is necessary to look at many genome assemblies at the same time to see which ones have non-target organisms present in them such as contaminants, parasites, symbionts, and so on.

For example, a researcher working on birds may want to see what genes are present in all bird genomes to study their evolutionary history. She would typically first retrieve all high quality bird genomes available publicly. But what if some of these genome assemblies had other species present in them? In that case her downstream analyses would have problems because some of the genes might actually be from non-bird genomes.

The BTK pipeline step 2.8 Where did the BTK plots come from is run on all publicly available eukaryotic genome assemblies. Although many submitters check their assemblies before releasing them, some don’t. Therefore it is vital to use BTK to assess the cleanliness of any genomes before retrieving them for further research.

BTK viewer can explore multiple genome assemblies at the same time to identify any non-target organisms are present. In the next step we will use the “Datasets” top menu option to explore summary statistics of the presence of contaminants or cobionts in different assemblies.

© Wellcome Connecting Science
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Eukaryotic Genome Assembly: How to Use BlobToolKit for Quality Assessment

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