Swarm v2: highly-scalable and high-resolution amplicon clustering

Swarm v2: highly-scalable and high-resolution amplicon clustering

Blog Article

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency.Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs.Here we present Swarm australis palette v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.

g., singletons and doubletons) onto larger ones.Swarm v2 also directly integrates the clustering and grahams c+ eczema & dermatitis cream breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.