Dada2 trimming for illumina 341F/805R primers

Can you share the quality plot with us from the sequences?

Personally instead of trim-left/right I prefer to trim primers by using a tool like cutadapt as discussed here.

We won't know if you need to truncate to a specific length without seeing the quality plots. But if the data was generated on the novaseq platform it may be that you don't need to trim due to the improved quality of the reads. If that is the case I advise reading up on the limitations of using dada2 with novaseq data as discussed here and in the hyperlinks in that post. Having said that the conclusion of the github thread is it should be fine but be wary, but hopefully this will be confirmed/fixed officially soon.

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