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PICRUSt2

Welcome to the PICRUSt2 website! 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 clustered 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.

If you come across and issues or you have comments, please post to the picrust google group.

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.