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