Daniel Lundin

I've done some testing that I'm summarizing here. 1. Stage the following files: https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm https://raw.githubusercontent.com/tseemann/barrnap/master/db/bac.hmm https://data.gtdb.ecogenomic.org/releases/latest/genomic_files_all/ssu_all.tar.gz (or the representatives, though quite few archaeal SSU sequences from representative genomes are complete...

Why not?! :+1:

This is fundamental in #magmap. We take either a set of user-supplied genomes that is sketched, a set of ready-made sketches (e.g. GTDB) or both, then submit the selected set...

I would absolutely recommend Decontam. We have seen in actual projects that raw removal of ASVs found in negative controls risks both to remove true ASVs found in samples and...

> Just as a comment, now PhytoRef (plastid sequences) are integrated into PR2 version 5.0.0. Also some errors have been corrected. So I think it is better to retire PhytoRef....

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...

I would say so, yes.

To me, adding columns to the sample sheet sounds best.

These were exactly the questions I had when I looked at the code, and more or less the way I would choose to go ahead. It would mean that no...

> > These were exactly the questions I had when I looked at the code, and more or less the way I would choose to go ahead. It would mean...