QIIME 2

QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. Since QIIME 1 is no longer supported officially (see announcement at http://qiime.org), it's not installed on the Ubuntu system of HPCC. The way QIIME 2 is installed and run on the HPCC Ubuntu is through conda https://docs.qiime2.org/2024.10/install/native/.

Below is how to install QIIME 2 (version 2018.2) in your home directory via conda:

Install QIIME 2

module purge
module load Miniforge3
conda env create --name qiime2-amplicon-2024.10 --file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2024.10/amplicon/released/qiime2-amplicon-ubuntu-latest-conda.yml

conda activate qiime2-amplicon-2024.10
qiime --help # test if installation is successful
qiime info
# all your QIIME commands go here
conda deactivate

Example of analysis

The example below is from a previous version of the current tutorial.

# Setup environment
module purge
module load Miniforge3
conda activate qiime2-amplicon-2024.10

# Obtain data for tutorial
mkdir qiime2-moving-pictures-tutorial
cd qiime2-moving-pictures-tutorial
wget -O "sample-metadata.tsv" "https://data.qiime2.org/2024.10/tutorials/moving-pictures/sample_metadata.tsv"

# Run tutorial 
mkdir emp-single-end-sequences
wget -O "emp-single-end-sequences/barcodes.fastq.gz" "https://data.qiime2.org/2024.10/tutorials/moving-pictures/emp-single-end-sequences/barcodes.fastq.gz"
wget -O "emp-single-end-sequences/sequences.fastq.gz" "https://data.qiime2.org/2024.10/tutorials/moving-pictures/emp-single-end-sequences/sequences.fastq.gz"

qiime tools import \
  --type EMPSingleEndSequences \
  --input-path emp-single-end-sequences \
  --output-path emp-single-end-sequences.qza

qiime tools peek emp-single-end-sequences.qza
# Expected Output:
# UUID:        593a4a7d-1cf5-46d6-b3c8-ca39810dc842
#Type:        EMPSingleEndSequences
#Data format: EMPSingleEndDirFmt

qiime demux emp-single \
  --i-seqs emp-single-end-sequences.qza \
  --m-barcodes-file sample-metadata.tsv \
  --m-barcodes-column barcode-sequence \
  --o-per-sample-sequences demux.qza \
  --o-error-correction-details demux-details.qza

qiime demux summarize \
  --i-data demux.qza \
  --o-visualization demux.qzv

qiime tools view demux.qzv

A full list of tutorials for QIIME2 can be found on the QIIME2 website and there is also list of plugins for QIIME2 for handling tasks such as trimming adaptors, demultiplexing, and denoising.