Hi @camzdel,
Currently there is no way to merge non-overlapping reads in Qiime2. This is often not a recommended way to handle paired-reads so I’m not sure if this will even be a supported function any time soon. For this you’ll have to look for a tool outside of qiime2, and unfortunately I don’t have any experience with this to give any recommendations either. Perhaps others can comment.
The merge-seqs isn’t used for merging reads in the way you’re thinking, but instead its used for combining some separate sequences, say from a few different runs, into one artifact.
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