DADA2 multiple sequencing runs - de novo picking allows for merging after artifact?

[Nicholas_Bokulich]

@ben

If we wanted to re-do with UCLUST tree-based closed or open picking, the merging of MiSeq files should be done prior to this step?

correct, if you use dada2 or deblur, merge the feature table and reference sequences after denoising.

for OTU picking, merging sequences is easiest before OTU picking but can be done afterwards (that is one advantage of closed-reference OTU picking, actually).

open-reference OTU picking can also be done sequentially (e.g., if you have an old dataset that you want to compare to a new one). cluster-features-open-reference outputs a new-reference-sequences file, which contains the reference sequences plus the new de novo OTUs. Use this file as the reference-sequences for the next set of sequences. You can then merge those feature tables and sequences together.

@ben

• If so, is there a guide? Or is it the same way we merge in QIIME1? (in other words, use QIIME1 to perform this).

We have a guide on otu picking but not for merging multiple runs, as I described above. You can also use qiime1 (or method of choice) to merge your sequences prior to importing to QIIME 2 if that is your preference.

@ben

Creation of a tree? The phyloqenetic tree is treated after the DADA2 step, however if we decide on a denote tree creation, is there a way that the tree can be matched with a known tree created from something like Greengenes or SILVA?

sounds like you are looking for q2-fragment-insertion. Head over there and see the tutorial linked from that post for more details.

I hope that helps!