how to import these reads: Mixed-oriented or not?

[SoilRotifer (Mike Robeson)]

Hi @Wieneke,

Running the cutadapt command is only removing the primers from the sequences, not demultiplexing. Though cutadapt has some demultiplexing options. If those are not appropriate for your data, you can try this approach:

Demultiplexing paired end MiSeq with mixed orientation

Hi @Danyl_McLauchlan, Great question. I know some folks with mixed-orientation barcoded reads use this tool to extract the barcodes and orient the reads prior to importing to QIIME 2 (possibly by doing two passes through this tool? I have not looked): GitHub - najoshi/sabre However, since you have combinatorial dual-indexed reads that complicates matters, so I'm not sure if sabre will cover your needs but it's worth a look. If any of the qiime1 virtual machines are still around, you may be a…

-Mike