QIIME2

QIIME2 is a bioinformatics platform used for the analysis of microbiome data.

The software package is made available on the UFS HPC via a conda environment which can by loaded as a module.

UFS HPC Usage Example

Follow these steps to start using QIIME2:

  1. Start a qwiz or qvnc session. If using a qvnc session, open the Terminal.

  2. Load the QIIME2 module (current version is 2022.2):

    $ module load life-sciences/qiime2

  3. Initialize the QIIME2 environment:

    $ qiime2_init

  4. Use QIIME2 as advertised.

Performance Notes

Memory and number of cores will depend and thus vary with the size of a dataset. However, the recommendation below is a good starting point.

  • 1 Node
  • 16 cores
  • 32 GB RAM

Benchmarks

No benchmarks are available.

UFS HPC Community Guides and Tutorials

  • No community guides are available.

Official site and documentation

Licensing Information

Primary citation

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., ... & Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology, 37(8), 852-857.

Pipeline component citations

To find a list of citations for the components of the QIIME2 pipeline, go to this page

Please remember to cite any additional methods used.

External Guides and Resources