– Download PICRUSt precalculated files


Downloads the PICRUSt precalculated files and stores them in the PICRUSt data directory.

Note that the script will skip downloading files already in the data directory (unless the --force argument is used).

Usage: [options]

Input Arguments:



Download the files again (i.e. overwrite any existing ones) [default: False]
-g, --gg_version
Version of GreenGenes that was used for OTU picking. Valid choices are: 13_5, 18may2012 [default: 13_5]
-t, --type_of_prediction
Type of functional predictions. Valid choices are: ko, cog, rfam [default: ko]
Download the precalculated files that allow confidence interval calculations for metagenome predictions. Only available for GreenGenes 13_5. [default: False]


Files are downloaded and stored in PICRUSt’s internally used data directory.

Download the default files (GreenGenes 13_5, KEGG KOs):

Download the default files (GreenGenes 13_5, KEGG KOs) and the files necessary for calculating confidence intervals: --with_confidence

Use GreenGenes 18may2012 and COG: -g 18may2012 -t cog