q2-vsearch clustering -- missing required files for the command

Hi,

I used to use dada denoise plugin in Qiime2, but I want to compare the output of postprocessing when using ASV versus OTU clustering method. I checked q2-vsearch which requires seqs.qza input:

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

After importing my sequence files using the Casava 1.8 paired-end demultiplexed fastq command, I have obtained a file named demux-paired-end.qza. So, what is meant by seq.qza used in the above command?
I know to generate representative sequences (rep_seq.qza), and feature table I need to apply DADA2 first. However, I prefer to use the clustering option instead.

So, how can I apply q2_vsearch after importing sequences?

Thanks!

Hi Eman!

Good idea. For my own notes, here is the tutorial for OTU clustering in Qiime2 using vsearch:
https://docs.qiime2.org/2024.5/tutorials/otu-clustering/

Yes!

If you have paired end reads you may want to start this process with joining.
https://docs.qiime2.org/2024.5/tutorials/read-joining/

So import > join > derep > cluster

Let us know if you have questions along the way!

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