It is often desirable to remove clusters with few sequences (either singletons, i.e. clusters with only one sequence, or clusters with a low number of sequences) . This can be done using USEARCH.
Alternatively, our in-house Java scrip 'OTUClusterSizeFiltering' can be used to remove such clusters. This program will run on Linux, Windows or MacOS. Download this script here, and run it without arguments to get usage information:
java -Xmx2G -jar OTUClusterSizeFiltering.jar
(The -Xmx2G option allows the program to use 2 gigabyte of memory, increase it if necessary)