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

[Eman (Eman Khalaf)]

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!

[colinbrislawn (Colin J Brislawn)]

Hi Eman!

@Eman

I want to compare the output of postprocessing when using ASV versus OTU clustering method.

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/

@Eman

So, what is meant by seq.qza used in the above command?

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!