Thank you for the reply! You are correct that I am picking up at the .fna/.qual node of the flowchart, however other versions of this lab's charts include "FASTA / Qual Prepared for QIIME" as an end step from the "Quality Checking / Demultiplexing" node, so I am trying to figure out what I am working with.
From Importing and Demultiplexing Sequence Data Quick Reference, and the QIIME2 Import Tutorial, it appears that I need to know if the data are multiplexed or not.
Where I am at:
Barcodes in Sequence (If they are only at the beginning, does that always imply single-end?)
Multiplexed? I think it is multiplexed, as several sequences share the same Barcode?
Need to strip out Barcodes to a metadata file for QIIME2 import?
Thanks for your time and input.