I am looking through the qiime2 tutorials and it seems that they are mostly focused on analyzing amplicon sequencing data. Are there established pipelines for analyzing whole-genome sequencing data for taxonomy/frequency features with qiime2, or are there better choices for that?
Cheers
Welcome to the forum @robmaz!
For shotgun metagenome sequencing? (that's my assumption since you mention taxonomy)
If yes, there are two QIIME 2 plugins right now for this:
https://library.qiime2.org/plugins/q2-metaphlan2/12/
https://library.qiime2.org/plugins/q2-shogun/15/
If you want WGS of a single organism, QIIME 2 does not currently have the functionality for, e.g., genome assembly.
I hope that helps!