Filter rep-seq.qza based on filtered feature table


I am sure this has probably been covered elsewhere, but I am struggling to find the clear direction. I have a filtered feature table from a really large data set. To cut down tree processing time, I would like to filter the matching rep-seq.qza prior to phylogenetic tree generation. Is there a clear method for doing this?

Sorry for a no doubt repeated post.


Hi @black.beaker,
To filter sequences such as your rep-seqs.qza you can use the qiime feature-table filter-sequences and feed your feature table to retain features only present in that feature table.


Cheers, think I have it up and running!

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