QIIME 2 2017.12 has a new cutadapt plugin which provides demux-single and demux-paired for demultiplexing reads where the barcodes are included within your reads!
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QIIME 2 2017.12 has a new cutadapt plugin which provides demux-single and demux-paired for demultiplexing reads where the barcodes are included within your reads!