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otutab_norm command
Commands > OTU analysis

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

Normalize OTU table counts to same number of reads per sample. Input must be in QIIME classic format. The -output option gives a filename for the result.

The number of reads per sample is specified by the -sample_size option. Default is 10000.

The adjusted count is calculated as new = (old * sample_size) / total where total is the total number of reads in the sample. The new count is rounded to the nearest integer, and the new total may be slightly different from sample_size due to rounding.

Samples with fewer than sample_size reads are scaled up, not deleted. To delete samples with too few reads, use the otutab_trim command.

It might be good idea to use a sample_size value which is, say, 2x or more larger than the typical sample size in the table to reduce rounding issues in small counts. On the other hand, it can also be a good idea to remove counts with frequencies lower than around 0.5%; see otutab_trim command for discussion.


usearch -otutab_norm otutable.txt -sample_size 5000 -output otutab_norm.txt