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Predict Metagenome (version 1.1.1.0)

Input biom file that is output of normalize_by_copy_number.py:

Select precalculated file from:

Precalculated input marker gene copy number predictions on per-otu basis:

Format of the output BIOM file:

Normalize by function?:

Normalizes the predicted functional abundances by dividing each abundance by the sum of functional abundances in the sample. Total sum of abundances for each sample will equal 1

Normalize by OTU?:

Normalizes the predicted functional abundances by dividing each abundance by the sum of OTUs in the sample. Note: total sum of abundances for each sample will NOT equal 1

Calculate accuracy metrics:

requires that per-genome accuracy metrics were calculated during genome prediction (predict_traits tool) (e.g. there are NSTI values in the genome biom file metadata)

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.

For more information please visit:

PICRUSt Documentation: https://picrust.github.io/picrust/
PICRUSt GitHub: https://github.com/picrust/picrust/
PICRUSt Support: https://groups.google.com/d/forum/picrust-users

Reference Data

Precalculated files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/

Command Documentation

This module produces a 'virtual' metagenome of functional abundances for each sample in the given OTU table. Choose either the KEGG Ortholog (KO), Clusters of Orthologous Genes (COG), or non-coding and other structured RNA (Rfam) precalculated files.

Input file: This should be a normalized OTU table populated by the output of the PICRUSt Normalize by Copy Number module.

Make sure that you specify an appropriate functional database for this command (usually the ko, cog, or rfam v13_5 database).