QIIME 2

Introduction

QIIME 2 is a is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results.

For more information, please check its website: https://quay.io/repository/qiime2/core and its home page: https://qiime2.org/.

Versions

2021.2
2022.11
2022.2
2022.8
2023.2
2023.5

Commands

qiime
python
python3

Module

You can load the modules by:

module load biocontainers
module load qiime2

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run QIIME 2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=qiime2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers qiime2

qiime metadata tabulate \
    --m-input-file rep-seqs.qza \
    --m-input-file taxonomy.qza \
    --o-visualization tabulated-feature-metadata.qzv