Can I run QIIME2 on Multiplexed 16S ONT files?

Hi @Chenyu,

We don't have a baked-in way to demultiplex these (they kind of are demultiplexed in as much as the barcodes are identified already).

But there's a pretty recent tool: PRONAME: Enhancing Taxonomic Accuracy with Nanopore Long-Read Metabarcoding and QIIME2 which looks to handle the upstream processing and generates Q2 results somewhere in the middle of that process. So I might give that whirl and see if it helps.

cc @BDubois

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