Trim primers from more than one amplicon with cudadapt in Qiime2?


I wish to use Cutadapt in Qiime2 to trim primers from demultiplexed, paired-end data that has reads for two different amplicons (a mix of 16S and 12S amplicons from vertebrate DNA in each sample).

Is it possible to trim F and R primers from both amplicons using Cutadapt in Qiime 2?

I have done it in the past with the standalone Cutadapt by first running a command with the primers from the first amplicon, and having all reads that were not trimmed (did not possess these primers) output to a separate directory. Then I would run a command with the primers from the second amplicon on the untrimmed directory. This would allow me to trim primers for both amplicons, and separate reads from each amplicon for each sample.

Is it possible to do something similar to this in Qiime2? If so how?


Hello Torrey,

I think your initial approach of running Cutadapt twice should still work in Qiime 2. Take a look at all these settings offered by the Qiime 2 Cutadapt plugin.

On a more general note, when I have amplicons from different regions I process them separately. You could do this too by using the deblur plugin to filter out just the 16S reads and just the 12S reads.

Let me know if this helps answer your question,


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Thanks Colin,
In the cutadapt plugin setting, there is an output for the trimmed sequences:
–o-trimmed-sequences ARTIFACT

But I don’t see how to also output the untrimmed sequences?
How would I output the untrimmed reads to a separate directory so that I can process them a second time in cutadapt to remove the primers from my second amplicon?

Good point. It looks like every sequence will get trimmed with the one set of primers you pass. This is tricky as you want to process twice (once for each primer).

I’m not sure how best to do this with cutadapt plugin for qiime 2. Maybe this would be easier to do using cutadapt directly, like you have done in the past. Then you could import into qiime.

Maybe one of the qiime devs will have other suggestions about how to do this!


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Hey there @Trodgers! As @colinbrislawn mentioned, you might make the quickest progress by using cutadapt directly (fortunately it is already installed in your QIIME 2 env!). We have an open issue regarding this missing output:

Stay tuned! :qiime2: :t_rex:

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