Is there a method to skip denoising and make table.qza and rep-seqs.qza?

[Daniel_Pass]

I am using some mock data that has non-standard quality profiles and I want to just skip the denoising step that wouldn’t make sense, but I can’t work out how to do this without using dada2 or deblur.

Lots of experience with qiime1, first time using qiime2.

Thanks

[jakereps (Jorden Kreps)]

You could possibly use q2-vsearch's dereplicate-sequences method. CLI would be something like:

$ qiime vsearch dereplicate-sequences \
  --i-sequences demux.qza \
  --o-dereplicated-table table \
  --o-dereplicated-sequences rep-seqs

Documentation can be found here!

[Daniel_Pass]

Thanks, that has worked perfectly. I would perhaps suggest putting a mention of that option in the tutorials because I couldn’t see any route from sequences to table/rep-set that didn’t include denoising. It seems that several questions on the forum are having the same problem, and “vsearch” isn’t the easiest name to interpret the function of.

Regards

[gregcaporaso]

Hi @Daniel_Pass,
To add to @jakereps’s suggestion, I think you probably do want to do some sort of basic quality filtering on your data, even if not using one of the denoising approaches. If so, you can perform QIIME-1-like quality control using the methods in the quality-filter plugin, and you can remove chimeric sequences as illustrated in the chimera checking community tutorial. We also do have some documentation on using dereplicate-sequences, as well as QIIME-1-like clustering methods, in the clustering sequences community tutorial.

We plan to migrate those community tutorials into the official documentation before too long so they’re easier to find (the Community Tutorials category is often used as a temporary spot to publish tutorials that are on their way into the docs but not quite ready yet).

Hope this helps!