Timming primers while seperating multiple markers with cutadapt in QIIME2?


I have a dataset with multiple markers (4) that were combined prior to indexing.

I would like to use cutadapt to a) trim primers, and b) separate reads from each marker.

I have done this before in the standalone cutadapt, but is it now possible to do it within QIIME2? I know that it was not last time I checked, but was wondering if it is now possible in the new version.

I have been trying to interpret open issues #10 and #29 as they seemed relevant, but with my limited knowledge I was not able to fully understand the outcome.

Basically, what I would like to do is trim primer set #1, and have the untrimmed reads outputted to their own artifact. Then I would run cutadapt again for primer set #2 on that “untrimmed" artifact, and then repeat for primer sets 3 and 4, until I have 4 separate artifacts with primers trimmed for each marker.

Does this make sense, and is it now possible in QIIME2?

Good morning Torrey,

Working with multiple marker genes at once is tricky. There is not a ‘built-in’ way to do this with Qiime 2, but I think you are on the right track with exploring these options.

This could work! I think it’s also worth considering b) separate first then a) trim.
This could be elegant because you could separate out your reads into 4 groups, then import them into qiime one at a time with their own trimming settings like normal 16S reads.

You could use an aligner (say vsearch) to compare each set of reads against it’s target region, then just use the database hits for trimming. Maybe like this:

vsearch --usearch_global reads.fna --db marker1.fna --id 0.80 \
--matched reads.marker1at80.fna \
--notmatched reads.not.marker1at80.fna

For my own notes, here are issues #10 and #29. These now appear closed…