As far as I can tell,
qiime feature-table filter-seqs is currently not included in the filtering data documentation. It would be helpful to include this command in the documentation. Based on the current documentation, it’s not clear how a user would filter sequences based on a filtered feature-table.
For instance with my own dataset, I filter ~30% of the sequence variants from the feature table (based on low prevalence across samples), but I didn’t know how to remove the sequence variants for the sequences artifact in order to match the filtered feature table. Given how slow taxonomic classification is with QIIME2, I want to trim my sequences down to match my filtered feature table prior taxonomic classification. I didn’t understand how to do this based on the “Filtering data documentation”