Thank you for your reply!
What filter-features allows us to do is to also filter our sequences file by passing in features-to-filter.tsv (see the forum post for how that file is generated) as metadata.
So do I understand correctly, when you use the filter-table filter-features command, both the feature table and the representative sequences file will be filtered according to the metadata file that is passed? I had another look at the filter-features documentation page and it only mentions a filtered table as output, not a filtered sequences file.
What I would be interested in was what Fernando Stuart mentioned in this post -- filtering the rep seqs file in order to build a phylogenetic tree containing only the sequences that remain after filtering out those found in lab controls.
Looking at the feature-table filter-seqs documentation, it seems like maybe this could be achieved using this command and passing in the same metadata file (i.e. list of features, not of actual sequences, to exclude) that would be used in filter-features? Is that right?
Thanks for your help!