QIIME2¶

The QIIME 2 bundle is used for next-generation microbiome analysis.

Software	Version
qiime	2023.5.1
rstudio	2022.12.0+353

UFS HPC Usage Example¶

The following command can be executed in the terminal to load the bundle:

1	`module load qiime`

The qiime cli and rstudio can be run as shown as below:

1 2	`qiime rstudio`

The qiime_shell commmand can be used to access a shell in the qiime bundle.

1	`qiime_shell`

Cloning the conda environment¶

If additional packages are required then the conda environment can be cloned to your home. Run the qiime_shell command and run the following commands in the qiime shell:

conda create --name qiime++ --clone qiime
conda activate qiime++
conda install -q -c conda-forge spyder

The name qiime++ can be changed to your needs and spyder can be adjusted to your needs. The new environment can be accessed as follows:

ERN_OVERRIDE_CONDA_ENV="qiime++" qiime

Finally, creating the clone can be scripted using a HERE-DOC in Bash

qiime_shell <<SCRIPT
. /ern/bin/activate
conda create --name qiime++ --clone qiime
conda activate qiime++
conda install -q -c conda-forge spyder
SCRIPT

The environment can be removed as shown below:

qiime_shell <<SCRIPT
. /ern/bin/activate
conda-env remove -n qiime++
SCRIPT

Performance Notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

UFS HPC Community Guides and Tutorials¶

No community guides available.

Official site and documentation¶

Licensing Information¶

QIIME2 is licensed under the BSD 3-Clause license.

Primary citation¶

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, and Caporaso JG. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37: 852?857. https://doi.org/10.1038/s41587-019-0209-9

External Guides and Resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za