Chapter 6 Picrust2

Firstly, prepare files for input into picrust2. Note: Will need to be in qiime conda environment for qiime commands to work.

$ mkdir picrust2

# export table.qza -> outputs as feature-table.biom
$ qiime tools export  \
--input-path DADA2_denoising_output/table.qza \
--output-path picrust2

# export rep seqs sqz -> outputs as dna-sequences.fasta file.
$ qiime tools export  \
--input-path DADA2_denoising_output/representative_sequences.qza \
--output-path picrust2

Install/activate picrust

$ conda create -n picrust2 -c bioconda -c conda-forge picrust2=2.3.0_b
$ conda activate picrust2

Now run picrust, full pipeline:

$ cd picrust2

$ picrust2_pipeline.py -s dna-sequences.fasta -i feature-table.biom -o picrust2_out_pipeline -p 1

# add descriptions (make easier in STAMP)
$ cd picrust2_out_pipeline/

$ add_descriptions.py -i EC_metagenome_out/pred_metagenome_unstrat.tsv.gz -m EC \
                    -o EC_metagenome_out/pred_metagenome_unstrat_descrip.tsv.gz

$ add_descriptions.py -i pathways_out/path_abun_unstrat.tsv.gz -m METACYC \
                    -o pathways_out/path_abun_unstrat_descrip.tsv.gz

These files are now ready for download and visualsation in STAMP.