Figure 1. Schematic view of Swarm’s clustering and refinement approach.

(A) Swarm clusters amplicons iteratively by using a small user-chosen local threshold, d, allowing OTUs to grow to their natural limits, where no other amplicons can be added. (B) Swarm takes into account the abundance of each amplicon to produce higher resolution clusters, by not allowing the formation of amplicon chains. The darker the red, the higher the abundance. (C) The fastidious option avoids under-grouping (e.g., the production of small OTUs such as singletons and doubletons) by postulating the existence of virtual linking amplicons to graft smaller OTUs onto larger ones.