I would like to find out the version of cutadapt distributed with Qiime2 version 2019.10.0 (latest version) and whether this version is now compatible with combinatorial dual barcodes?
############
qiime cutadapt --version
QIIME 2 Plugin ‘cutadapt’ version 2019.10.0 (from package ‘q2-cutadapt’ version 2019.10.0)
Just following up. I have tried to use cutadapt in qiime2 v2019.10 with combinatorial barcodes. I can confirm it is behaving the same way as reported in the previous thread: https://forum.qiime2.org/t/does-q2-cutadapt-support-dual-indexed-reads/11708/21. The result only demultiplexed samples with a first unique instance of the forward barcode, but ignored the rest. I have 130 samples, but only 16 samples demultiplexed.
At this time I do not believe the cutadapt plugin with latest version of qiime2 to be compatible with combinatorial dual barcodes.
Any suggestions other than making multiple metadata sheets, as suggested in the original post?
Thanks,
Amber