tablerareΒΆ

$ micca tablerare --help
usage: micca tablerare [-h] -i FILE -o FILE -d DEPTH [-r] [-s SEED]

Rarefy an OTU table by subsampling, with or without
replacement. Samples that have fewer counts then the depth are
omitted from the output table. OTUs that are not present in at
least one sample are omitted from the output table.

optional arguments:
  -h, --help            show this help message and exit

arguments:
  -i FILE, --input FILE
                        input OTU table file (required).
  -o FILE, --output FILE
                        output rarefied OTU table file (required).
  -d DEPTH, --depth DEPTH
                        sample depth (>0, required).
  -r, --replace         subsample with replacement.
  -s SEED, --seed SEED  random seed (default 0).

Examples

Rarefy an OTU table at a depth of 1000 sequences/sample:

    micca tablerare -i otutable.txt -o otutable_rare.txt -d 1000