does q2-cutadapt support dual indexed reads?

[Nicholas_Bokulich]

@LuSanto

Semantic type SampleData[MultiplexedPairedEndBarcodeInSequence] does not have a compatible directory format.

The manifest format implies that your reads are already demultiplexed, so is incompatible with the MultiplexedPairedEndBarcodeInSequence format.

See here for an importing example (you will need to adjust of course for paired-end, since this is a single-end example but same idea):

Demultiplexing and Trimming Adapters from Reads with q2-cutadapt

NOTE This tutorial is a work in progress, and is incomplete at the moment. It demonstrates at a high level some of the methods available in the q2-cutadapt plugin available in QIIME 2 2018.2. Please stay tuned here for additional updates as this tutorial is expanded upon in the coming weeks. Multiplexed reads with the barcodes in the sequence reads can be demultiplexed in QIIME 2 using the q2-cutadapt plugin, w…