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PICRUSt2

Welcome to the PICRUSt2 wiki! Here you will find descriptions of the scripts, installation instructions, and workflows. See the right side-bar for details.

We are planning to publish PICRUSt2 by the end of 2018. It includes these and other improvements:

• Allow users to predict functions for de novo sequences (e.g. DADA2 and deblur output) by taking a sequence placement approach
• Updated pre-calculated files with additional genomes and gene families.
• Addition of hidden-state prediction algorithms from the castor R package.
• Allows output of MetaCyc ontology predictions that will be comparable with common shotgun metagenomics outputs.
• Inference of pathway abundances now relies on MinPath, which makes these predictions more stringent.

PICRUSt2 Flowchart

Citations

PICRUSt2 wraps a number of tools to generate functional predictions from amplicon sequences. If you use PICRUSt2 you also need to cite the below tools.

For phylogenetic placement of reads:

• PaPaRa
• EPA-NG
• gappa, which is based on the genesis library.

For hidden state prediction:

• castor

For pathway inference:

• MinPath - A modified version of this tool from the HMP project is also packaged with PICRUSt2. This tool was releasd under the GNU General Public License. Source code.