tablestatsΒΆ

$ micca tablestats --help
usage: micca tablestats [-h] -i FILE [-o DIR] [-t STEP] [-r] [-s SEED]

micca tablestats reports a sample summary, an OTU summary and
the rarefaction curves for the input OTU table. The
rarefaction curves are evaluated using the interval of 'step'
(-t/--step) sample depths, always including 1 and the total
sample size.

micca filterstats returns in the output directory 4 files:

* tablestats_samplesumm.txt: samples summary;
* tablestats_otusumm.txt: OTUs summary;
* tablestats_rarecurve.txt: rarefaction curves in text format.
* tablestats_rarecurve_plot.txt: rarefaction curves in png format.

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

arguments:
  -i FILE, --input FILE
                        input FASTQ file, Sanger/Illumina 1.8+ format
                        (phred+33) (required).
  -o DIR, --output DIR  output directory (default .).
  -t STEP, --step STEP  sample depth interval (for rarefaction curves, default
                        500).
  -r, --replace         subsample with replacement (for rarefaction curves).
  -s SEED, --seed SEED  random seed (for rarefaction curves, default 0).

Examples

Compute OTU table statistics on otutable.txt: 

    micca tablestats -i otutable.txt -o tablestats