PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
The PICRUSt project aims to support prediction of the unobserved character states in a community of organisms from phylogenetic information about the organisms in that community. The primary application is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.
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Reference Data
Precalculated files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/
Command Documentation
Compare an observed table to an expected table using either relative abundance or real counts.
Input files:
Observed table: A table of observed relative abundances or real counts in .biom format.
Expected table: The expected table of relative abundances or real counts in .biom format.
Output file: Tab delimited file with various accuracy metrics.
Optional Parameters:
compare observations
Calculate accuracy values by comparing between observations (instead of between samples) [default: False]
normalize
Convert both expected and observed tables to relative abundances (instead of observations) [default: False]
limit to expected observations
Ignore observations that are not in the expected table[default: False]
limit to observed observations
Ignore observations that are not in the observed table[default: False]
shuffle samples
Shuffle samples ids randomly before measuring accuracy[default: False]
not relative abundance scores
Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN [default: False]