qiime2
Link to section 'Introduction' of 'qiime2' 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/.
Link to section 'Versions' of 'qiime2' Versions
- 2021.2
- 2022.11
- 2022.2
- 2022.8
- 2023.2
- 2023.5
- 2023.7
Link to section 'Commands' of 'qiime2' Commands
- biom
- qiime
- python
- python3
Link to section 'Module' of 'qiime2' Module
You can load the modules by:
module load biocontainers
module load qiime2
Link to section 'Example job' of 'qiime2' Example job
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