DADA 2 : how to maximize the number of the total sequences in the final biom file?

Hello everyone, I first want to excuse myself if this kind of question as been posted before but the forum is quite big in contents so I searched but I didn't find something similar so I decided to ask.....
Talking in general, can somebody tell me the strategies or the steps that someone as to follow in order to have the maximum number of sequences in the final biom table?

I mean, there should be some "common guide line" about the things that someone should do to the reads before process them with DADA 2 (primer cut, quality control and so on..), general information on how to set the parameters of the DADA2 plugin and anything else that may be important in general...

Thank you to everyone!

Bye :slight_smile:

Hi @sleva88 - this is a huge question! Have you checked out some of our resources? We have put a lot of effort into answering these kinds of queries:

If you have a more specific question please come ask it here!


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