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)
Welcome to the forum, @damselflywingz!
The version distributed with the 2019.10 release was cutadapt=2.6
You can check what you have installed any time like so:
conda list | grep 'cutadapt'
Yes I believe it is compatible but maybe @ChrisKeefe or @thermokarst can comment.
Thank you for the quick response and the hint for getting the version of cutadapt from conda list. I will try to demultiplex within Qiime2 now
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?
16S_c.tsv (25.7 KB) SampleData[PairedEndSequencesWithQuality]2.qza.qzv (296.1 KB)
####ran the following command to demultiplex
source activate qiime2-2019.10
qiime cutadapt demux-paired --i-seqs demux-paired-end2.qza --m-forward-barcodes-file 16S_c.tsv --m-forward-barcodes-column Forward_barcode --m-reverse-barcodes-file 16S_c.tsv --m-reverse-barcodes-column Reverse_barcode --o-untrimmed-sequences MultiplexedPairedEndBarcodeInSequence --o-per-sample-sequences SampleData[PairedEndSequencesWithQuality] --output-dir /global/home/hpc4605/Raw_data/Tick16sMiSeq2019/MiSeq_from_David/Out_Qiime_import/Demux_cutadapt_out/demux_cutadapt.qza
(qiime2-2019.10) [[email protected] Out_Qiime_import]$ conda list | grep 'cutadapt'
cutadapt 2.6 py36h516909a_0 bioconda
q2-cutadapt 2019.10.0 py36_0 qiime2/label/r2019.10
That is correct.
Unfortunately not, sorry.