I’m running an analysis on a housekeeping gene. I was wondering if I can do some of my analysis in QIIME2. I will only have the sequences of that gene from my MiSeq run of each sample and the metadata of the samples. Would I be able to 1. Run fragment-insertion (let’s say I’ve found taxonomy that match to the sequences) 2. Run deblur 3. Run beta/alpha diversities 4. Run beta/alpha diversities that require a tree (can I do this without running deblur?)? Thank you.
Very interesting question, @Stephanieorch.
Meaning that you will not have a reference sequence database? (my answers below assume that is what you mean)
No, you need a set of aligned reference sequences to use this plugin.
No, deblur requires a set of reference sequences for positive filtering. dada2 and OTU picking would be options, however.
Yes, as long as you use non-phylogenetic methods.
No and no. No reference sequences, no tree.
Ok so then if I’m able to find a set of reference sequences I can do all of this?
If you want to use q2-deblur and q2-fragment-insertion, yes you will need reference sequences.
My answers above re: phylogeny assumed that you would be using q2-fragment-insertion to make that phylogeny. I should correct myself: you can do a do novo alignment of your sequences to build a tree and run phylogenetic alpha/beta diversity analyses (if a de novo alignment of those sequences provides adequate phylogenetic information) — no fragment insertion required.
You will also need reference sequences for taxonomy classification, so I would personally want to track some down anyway. But if you can’t do that, I would recommend just using dada2 and de novo alignment to build a phylogeny and then everything would be easy.