Help using PICRUSt2 pipeline?

Hello @sesamechicken

For the error here

Reviewing the error and input data would allow us to help to troubleshoot. You can paste back a generated shared history link to get this started!

Then, for this part of your question

The Help section of the tool form has a simplified guide and a link out to the author’s wiki site with more. The tools will work in Galaxy the same way!

PICRUSt2 Full pipeline (Galaxy Version 2.5.3+galaxy0)

Help

What it does

PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a tool for predicting functional abundances based only on marker gene sequences.

Read more about the tool: Home · picrust/picrust2 Wiki · GitHub

PICRUSt2 full pipeline

Run sequence placement with EPA-NG and GAPPA to place study sequences (i.e. OTUs and ASVs) into a reference tree. Then runs hidden-state prediction with the castor R package to predict genome for each study sequence. Metagenome profiles are then generated, which can be optionally stratified by the contributing sequence. Finally, pathway abundances are predicted based on metagenome profiles. By default, output files include predictions for Enzyme Commission (EC) numbers, KEGG Orthologs (KOs), and MetaCyc pathway abundances. However, the tool enables users to use custom reference and trait tables to customize analyses.

Note

The standard pipeline will generate metagenome predictions for 16S rRNA gene data.

Input

  1. A FASTA of amplicon sequences variants (ASVs; i.e. your representative sequences, not your raw reads)
  2. A BIOM table of the abundance of each ASV across each sample.

Output

  1. Output tree with placed study sequences.
  2. Metagenome Predictions
  3. Pathway level predictions

Please give this a review and let us know if you are able to resolve this on your own, or if you would like some help with a history review! :slight_smile:

Related Q&A → Search results for 'picrust2 order:latest' - Galaxy Community Help