Qiime2

Introduction

QIIME 2 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:

BioContainers: https://quay.io/repository/qiime2/core

Home page: https://qiime2.org/

Versions

• 2023.2

• 2023.5

• 2023.7

• 2023.9

Commands

• biom

• qiime

• python

• python3

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 qiime2 on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=qiime2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load qiime2/XXXX ### you can run *module avail qiime2* to check all available versions

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