UPARSE is a method for generating clusters (OTUs) from next-generation sequencing reads of marker genes such as 16S rRNA, the fungal ITS region and the COI gene. The clustering method itself is the UPARSE-OTU algorithm , implemented as the cluster_otus command in USEARCH . To run UPARSE in practice, you need to run a pipeline of USEARCH commands. FAQ: Should I use UPARSE (97% OTUs) or UNOISE (denoising)? Should I use OTU clustering or denoising (ASVs)?
Sometimes OTUs are more appropriate, sometimes ASVs are better; see discussion on FAQ page.
To make ASVs, use the unoise3 command in USEARCH.
Reference
Edgar, R.C. (2013) UPARSE: Highly accurate OTU sequences from microbial amplicon reads, Nature Methods [ Pubmed:23955772 , dx.doi.org/10.1038/nmeth.2604 ].
