Is there a way to convert SampleData[JoinedSequencesWithQuality] to SampleData[SequencesWithQuality]?
Converting types is not available nor desirable as it kind of defeats their purpose. They are meant to work as a check to ensure compatibility across plugins and avoid incorrect types being used. That being said, if you can give us a bit more detail about what you are trying to do and why you need the type to be different perhaps we can find an appropriate solution.
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