When clustering ASVs from deblur with VSEARCH, is it possible to know the membership of resulting clusters?

[jcmcnch (Jesse M)]

Update Oct 2020:

Please see the following post for updated and more complete instructions if this hacky method is of use to you:

vsearch de novo output --uc option

Thanks for the very interesting feedback @colinbrislawn, I spent a bit of time trying to figure this out myself the last few days, and I tested three possible routes towards classifying a set of sequences. I started with a file from a pile of bat guano data ( as is customary for me...), which had been denoised in QIIME via DADA2. So, a fasta file of about 9,000 representative sequence features/ASVs (let's call it repSeqs.qza). Using that file, I then tried the following: Export th…

Hi Nicholas and anyone else who might want this information:

The simplest way I could think of to do this was to just change line 183 "_cluster_sequences.py" to:

" with tempfile.NamedTemporaryFile(delete=False) as out_uc:"

This prevents the temp "uc" file generated by VSEARCH from being wiped at the end of the "with" loop. Once q2-vsearch is done the clustering, you can just copy it to a non-temporary file and you're off to the races. I tested it and the result looks good. Thanks again for your help!

Cheers,

Jesse