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