Selecting OTU picking methods in QIIME 2

Dear QIIME 2 users!
Is it possible to use or integrate other OTU clustering methods like sortmerna, mothur, trie, uclust_ref, usearch, usearch_ref, blast, usearch61, usearch61_ref, sumaclust, swarm, prefix_suffix, cdhit, uclust in QIIME 2 ?

Hi @Arun_kumar,
Welcome in the forum!
Currently aside blast, none of the other methods in your list are implemented as qiime2 plug in (as far I know at least ..).
This does not mean that could not be possible, only that nobody did yet.
However, all these methods output abundance table as well as a rpresentative sequence file. Hence, you could use them outside QIIME2 and then import their results for further analyses!

The qiime2 plug in implementing blast+ is aimed to taxonomic assignment, and therefore is not usable to produce OTUs.

Hope it helps

A further note on methods embedded in usearch, these are proprietary methods and so probably only hteir owner could embed them into a qiime2 plug in, however vsearch is aimed to be the free version for usearch, so they "should" give very similar results, and vsearch is available as qiime2 plug in!


I started looking for clustering methods in QIIME2 because QIIME1 had that option – OTU pickingΒΆ. Anyhow thanks for the information.

Hi @Arun_kumar,
if you are looking for de-novo clustering using qiime2, the following tutorial could be useful:


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