DADA2 Option Specification


I would like to make my ASV analysis with DADA2 more sensitive to different domains in the (bacterial) strains I've had sequenced - specifically the KS and AD domains rather than the 16s loci.
Is there a way to change the defaults with the DADA2 plug-in in QIIME2 so that this can be done?
I only see an option to tweak the trim and read length.

Thanks in advance!

Hi @Taylorr ,

dada2 is marker-gene agnostic, as far as I am aware. It trains its error model on the fly and assumes that all input sequences are from the same marker gene and primers, but otherwise can take any marker-gene sequences as input. So KS and AD sequences should be fine.

Good luck!


Oh, makes sense - I do recall coming across its agnostic approach to primers. So cool. Thanks a ton for this confirmation!

Taylor :wink:

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