You can provide a FeatureTable[Frequency] as input to feature-table filter-seqs, this will allow you to filter your FeatureData[Sequence] down to only the features present in your table.
:qiime2:
You can provide a FeatureTable[Frequency] as input to feature-table filter-seqs, this will allow you to filter your FeatureData[Sequence] down to only the features present in your table.
:qiime2: