Note that this command currently does not currently account for discarding singletons. I doubt it matters in practice, because other sources of error are probably more important, so rarefaction analysis has dubious value for marker gene OTUs. If you are interested in a rarefaction command which accounts for singletons, please let me know and I will implement the feature.
Input is an OTU table in QIIME classic format.
The -metric option specifies a metric name. Default is richness. See alpha diversity metrics for supported metrics.
The specified metric is calculated by subsampling the OTU table at 1%, 2% ... 99%, 100% of the reads. The -method option specifies which subsampling method to use. Default is fast subsampling. See otutab_subsample command for discussion of subsampling and supported methods.
The output file is specified by the -output option. The output file is a tabbed text file with a header followed by 100 lines, one per subsample size. The first field is the subsample size as a percentage.
The output file can easily be loaded into a spreadsheet or other charting software for generating figures.
usearch -alpha_div_rare otutab.txt -output rare.txt