Compatibility of DADA2 for ITS amplicon reads

[UniAlberta]

Hi Dr. Callahan,

I was wondering to ask if DADA2 is incompatible with ITS amplicon reads. I received a comment from a reviewer regarding this controversy. Im pretty sure its a valid pipeline when we don`t specify read length and remove primers with cutadapt.
I was wondering to hear your opinion about this and if I could use any literature to support this pipeline for ITS amplicon reads.

Thanks

[benjjneb]

Yes DADA2 is completely compatible with ITS data. There are some specific considerations related to trimming and filtering because ITS is such a variable-length region. We have published an ITS specific tutorial that shows one way to deal with ITS data: https://benjjneb.github.io/dada2/ITS_workflow.html

As for literature, there are many 100s of papers that have been published that used DADA2 for ITS data one could cite as examples. There are also evaluation papers of DADA2 for ITS data, one that quickly comes to mind is this one: https://doi.org/10.1016/j.funeco.2019.03.005

[UniAlberta]

Thank you so much for the clarification.