-
Notifications
You must be signed in to change notification settings - Fork 115
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Phylogenetic placement of ASVs #236
Comments
I've done some testing that I'm summarizing here.
Gappa can also be used to create Unifrac, aka Kantorovich-Rubinstein (KR), distances and many other things, so the |
Phylogenetic placement is now implemented in nf-core subworkflow |
Absolutely. There are a couple of things we should discuss regarding the implementation, particularly with regards to reference trees and alignments. I thought we could discuss that when we meet next month. |
Alright! |
Phylogenetic placement, using Pplacer, is a better way of getting a phylogenetic tree of short amplicons than making a phylogeny from an alignment of the ASVs on their own.
There's a QIIME2 module called q2-fragment-insertion for the purpose, or we can roll our own (see below). The builtin phylogeny in the QIIME2 module is "the 99% OTU Greengenes 13.8 tree with 203,452 tips", but I think one can specify ones own tree. Greengenes is, as you know, outdated.
Rolling our own would allow users to provide an alignment or hmm plus a phylogeny. The builtin would, I suggest, use GTDB species representative genome data. A problem here is that GTDB provides SSU sequences, but not a phylogeny built on them. We would therefore either have to estimate the phylogeny or assume that the protein alignment-based phylogeny is correct and build a reference SSU alignment from the sequences they provide.
Processing outline for GTDB:
hmmalign
to align to the hmms used e.g. by Barrnap and output only positions that match the profile. *)*) Candidates for nf-core modules.
The text was updated successfully, but these errors were encountered: