 Swarmv1 is a novel open-source Amplicon clustering program that produces fine-scale molecular operational taxonomic units, OTUs, without global clustering thresholds or input-order dependency. Swarmv2 has two new features, a linear scaling algorithm for D equals 1 and the fastidious option that reduces undergrouping by grafting low-abundant OTUs onto larger ones. Swarmv2 also directly integrates the clustering and breaking phases, dereplicate sequencing reads with D equals 0, outputs OTU representatives in faster format, and plots individual OTUs as two-dimensional networks. This article was authored by Frederick Mahet, Torbjorn Rohns, Christopher Quince, and others.