Installing PICRUSt

Description

PICRUSt is a bioinformatic tool developed to gain insight into the metagenomic function of the microbiome based on 16S rRNA amplicon data. By using know genomes and their genomic composition, PICRUSt inferres abundance of genes based on the abundance of OTU's. Using this method, you can attempt to infer microbial genomic potential without the need for costly Whole Metagenomic Shotgun Sequencing (WMS).

Step 1: Download the latest version PICRUSt and place the package in your HOME folder and start the MacQIIME environment.

# Start qiime
macqiime

# Download package into the home folder
wget -P $HOME https://github.com/picrust/picrust/releases/download/1.1.0/picrust-1.1.0.tar.gz

Step 2: Decompress the downloaded folder in your HOME directory.

# Decompress folder
tar -zxvf $HOME/picrust-1.1.0.tar.gz

Step 3: Once PICRUSt has been downloaded, you will need to download database files for referencing taxa to KEGG genes. Download the following 2 files and save them both in picrust-1.1.0/picrust/data directory.

# Make new directory to store required databases
mkdir -p $HOME/picrust-1.1.0/picrust/data

# Download 16S data
wget -P $HOME/picrust-1.1.0/picrust/data ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/16S_13_5_precalculated.tab.gz

# Download KEGG genes
wget -P $HOME/picrust-1.1.0/picrust/data ftp://ftp.microbio.me/pub/picrust-references/picrust-1.1.0/ko_13_5_precalculated.tab.gz

Step 4: Install PICRUSt on your system and enter the account password.

sudo pip install -e ~/picrust-1.1.0/

Step 5: Test the intallation by running the command below.

predict_metagenomes.py --version
#> Version: predict_metagenomes.py 1.1.0