Home Software Services About Contact usearch manual
otutab_subsample command
Commands > OTU analysis

See also
  OTU table
  OTU commands
  Making an OTU table (otutab command)
  otutab_norm command

Generate an OTU table by subsampling (also called rarefying). The subsampled table is the simulated result if fewer observations (reads) had been available. The input file must be in QIIME classic format.

The size of the subsample is specified by the -sample_pct option. E.g., if you set -sample_pct 50, this will make an OTU table assuming that half the reads had been generated.

To subsample to a fixed number of reads, use the otutab_norm command.

To make a rarefaction curve for one or more alpha diversity metrics, it is easier to use the alpha_div_rare command.

The output file is specified by the -output option. The output file is also in QIIME classic format.

The method to use is specified by the -method option. Valid values are fast (the default), with_replacement and without_replacement. For all methods except fast, the number of iterations is specified by the -iters option (default 32).

Fast subsampling
Uses a fast approximation to randomized subsampling.

With / without replacement
Subsamples using a random number generator. Counts are averaged over several iterations and rounded to the nearest integer. When replacement is allowed, a read may be selected more than once. If replacement is not allowed, a read may only be selected once.

Which method should you use?
There is some disagreement in the literature about whether subsamping / rarefaction should be performed with or without replacement. In my opinion, it doesn't matter because there are much bigger issues in intepreting counts, so I would suggest using the default fast approximation because all three methods usually give similar results.


usearch -otutab_subsample otutable.txt -subsample_pct 75 -output otutable_75.txt