Amplicon sequence variant

An amplicon sequence variant (ASV) is any one of the inferred single DNA sequences recovered from a high-throughput analysis of marker genes. Because these analyses, also called "amplicon reads," are created following the removal of erroneous sequences generated during PCR and sequencing, using ASVs makes it possible to distinguish sequence variation by a single nucleotide change. The uses of ASVs include classifying groups of species based on DNA sequences, finding biological and environmental variation, and determining ecological patterns.

ASVs were first described in 2013, by Eren and colleagues. Before that, for many years the standard unit for marker-gene analysis was the operational taxonomic unit (OTU), which is generated by clustering sequences based on a threshold of similarity. Compared to ASVs, OTUs reflect a coarser notion of similarity. Though there is no single threshold, the most commonly chosen value is 3%, which means these units share 97% of the DNA sequence. ASV methods on the other hand are able to resolve sequence differences by as little as a single nucleotide change, thus avoiding similarity-based operational clustering units altogether. Therefore, ASVs represent a finer distinction between sequences.

ASVs are also referred to as exact sequence variants (ESVs), zero-radius OTUs (ZOTUs), sub-OTUs (sOTUs), haplotypes, or oligotypes.