Discarded results produced by q2-cutadapt's trim-paired when working with mixed-orientation reads

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I forgot that the issue outlined here appears to have been fixed in qiime2-2020.11. So you should be fine.

However, if you ever run into a case in which you need to re-orient your sequences you can use RESCRIPt's orient-seqs command.

EDIT: I forgot that the orient-seqs command will currently only run on FASTA inputs. We hope to work on a solution for FASTQ.

-Mike