Hi @jessicalmetcalf! You can use the new q2-vsearch method dereplicate-sequences to convert your seqs.fna file to a FeatureTable[Frequency] and FeatureData[Sequence]! Check out @gregcaporaso’s draft community tutorial on q2-vsearch, in particular, the section titled “Dereplicating a SampleData[Sequences] artifact.”
Once you have those two new artifacts, you could either perform OTU clustering (see the rest of that draft tutorial), or continue on with generating summaries.
Hope that helps!