micca-filterΒΆ

Filters OTUs from an OTU table based on their observation counts.

$ micca-filter --help
usage: micca-filter [-h] [-v] [-m N] [-M N] input output

micca-filter filters OTUs from an OTU table based on their observation counts.

positional arguments:
  input          input OTU table file
  output         output OTU table file

optional arguments:
  -h, --help     show this help message and exit
  -v, --version  show program's version number and exit
  -m N, --min N  minimum total count per OTU (e.g., '-m 2' discards singletons
                 OTUs) (default 2)
  -M N, --max N  maximum total count per OTU (e.g., look at low abundance
                 OTUs) (default None)

Example:

 $ micca-filter otu_table.txt filtered.txt -M 200

micca v. 0.1.
Author: Davide Albanese <davide.albanese@fmach.it>
Fondazione Edmund Mach, 2014.

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