Workflow

Below is a brief overview of the PICRUSt2 workflow, which includes example commands for processing 16S sequencing data and getting E.C. number abundances. See the side-bar for more details on individual commands. This workflow is still being developed and will be improved and updated soon!

Note that you can type the option -h to get a description of each below script. Note that the below command

1. Place study sequences into reference phylogeny (details)

place_seqs.py -s STUDY_SEQs.fna -o OUTPUT.tre --threads 10 --out_dir placement_working

2. Run hidden-state prediction to get 16S copy numbers and E.C. number abundances per predicted genome (details)

hsp.py -i 16S -t OUTPUT.tre -o 16S_predicted -p 10

hsp.py -i EC -t OUTPUT.tre -o EC_predicted -p 10

3. Predict gene family abundances in sequencing samples (adjusts gene family abundances by 16S sequence abundance) (details)

metagenome_pipeline.py -i study_seqs.biom \
-m 16S_predicted_out.txt -f ec_predicted_out.txt \
-p 4 -o OUTPUT_DIR

4. Infer pathway abundances (details)

run_minpath.py -i OUT_PREFIX.genefamilies.biom \
               -m /path/to/picrust/MinPath/ec2metacyc_picrust_prokaryotic.txt \
               -o Pathway_abundances.tsv \
               --out_dir minpath_working \