Low abundance OTUs can eliminated from the OTU table if they have fewer than a given count across all the samples in the experiment.
To run the tool, go to
Toolbox | Microbial Genomics Module () | Metagenomics () | Amplicon-Based Analysis () | Remove OTUs with Low Abundance ().
Choose an OTU table as input, select the filtering parameters and save the table. The threshold for determining whether an OTU has sufficient abundance is specified by the parameters minimum combined abundance and minimum combined abundance (% of all the reads). The algorithm filters out all OTUs whose combined abundance across all samples is less than the minimum combined abundance or whose combined abundance is less than the minimum combined abundance (% of all the reads) across all samples. The default value for the Minimum combined abundance is set at 10.