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 here and there is also list of plugins for QIIME2 for handling tasks such as trimming adaptors, demultiplexing, and denoising.