– Normalize an OTU table by marker gene copy number


Usage: [options]

Input Arguments:



-i, --input_otu_fp
The input otu table filepath in biom format
-o, --output_otu_fp
The output otu table filepath in biom format


-g, --gg_version
Version of GreenGenes that was used for OTU picking. Valid choices are: 13_5, 18may2012 [default: 13_5]
-c, --input_count_fp
Precalculated input marker gene copy number predictions on per otu basis in biom format (can be gzipped).Note: using this option overrides –gg_version. [default: None]
Identifier for copy number entry as observation metadata [default: CopyNumber]
Instead of loading the precalculated file in tab-delimited format (with otu ids as row ids and traits as columns) load the data in biom format (with otu as SampleIds and traits as ObservationIds) [default: False]


A normalized OTU table

Normalize the OTU abundances for a given OTU table picked against the newest version of Greengenes: -i closed_picked_otus.biom -o normalized_otus.biom

Change the version of Greengenes used for OTU picking: -g 18may2012 -i closed_picked_otus.biom -o normalized_otus.biom