would it be possible to use qiime2 for estimating SNPs?

(Hajar) #1

Hi,
First, thanks a lot for your efforts and help.
I would like to know, if possible to estimate SNPs per each ASV (rep.seq) generated from dada2 algorithm.

I know that we can do that outside qiime2 but it is time consuming and sometimes alignment is not possible.

Just wondering if it can be also done inside qiime2. If yes which plugin shall I use?
Thanks a lot.
Hajar

#2

Hi! I don’t think that you can use Qiime for this purposes at all.