Gavin Douglas edited this page Oct 12, 2018 · 20 revisions

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

PICRUSt2 includes these and other improvements:

  • Allow users to predict functions for any 16S sequences. Representative sequences from OTUs or amplicon sequence variants (e.g. DADA2 and deblur output) can be used as input by taking a sequence placement approach
  • Database of reference genomes used for prediction has been expanded by >10X.
  • 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


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:

For hidden state prediction:

For pathway inference:

  • MinPath (paper, website) - A modified version of this tool from the HMP project is packaged with PICRUSt2. This tool was released under the GNU General Public License.
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