When clustering with swarm, when is an appropriate time to check for chimeras?
As pointed out by Colin Brislawn, Robert Edgar recommends using uchime to remove chimeras after OTU picking with uparse. His recommendation is based, in part, on chimera removal heuristics built in to uparse. When using uclust, Robert Edgar recommended referenced-based chimera checking before OTU picking so that OTUs were not influenced by chimeras. When using swarm with default parameters or low d values (i.e. high-resolution clustering), chimeras and non-chimeras should form independent OTUs. It is therefore more interesting to perform the chimera detection on OTU representatives, as the dataset size reduction allows to perform both de novo-and reference-based approaches.