Recommended defaults? about chopper HOT 5 CLOSED

Hi,

I would say that the defaults are highly dependent on the application, e.g. Assembly vs reference alignment

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What about assembly?

from chopper.

I don't know if I dare to suggest defaults that would work fine in most scenarios, e.g. duplex will have higher accuracy than simplex sequencing, you could filter a little more stringent on length for ultra-long libraries... Could you let me know which data type to expect?

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The most practical use case would be genome assemblies for microeukaryotes like yeast. The second most common use case would be larger amplicons like full length 16S. Last use case would be actual community wide full metagenomes.

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I can't propose defaults that would make sense in all those scenarios. This is difficult. I think the most correct would be to leave this to the end user, if possible.

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