Best approach for analyzing Sanger sequences from ITS2 region

Hi @jhines1!

That's correct. If you do not want to use OTU clustering, you can just use qiime vsearch dereplicate-sequences to dereplicate — that will give you a feature table and representative sequences artifact.

Yes... see this tutorial. Just follow the import and dereplicate-seqs steps in that section of that tutorial, then proceed through the ITS tutorial.

The feature table you get from dereplicate-sequences is all you need to proceed to diversity analyses. Denoising is important for correcting errors from next-generation sequencing methods, but since you have Sanger data and are doing a Sanger-specific QC protocol with Geneious, then denoising should not be necessary anyway.

I hope that helps!