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QIIME 2

The QIIME 2 bundle is used for next-generation microbiome analysis. The bundle packages version 2024.10. Four distributions are packaged: tiny, amplicon, metagenome, and pathogenome.

Usage example

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

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module load qiime

The amplicon, metagenome, and pathogenome distributions can be loaded as shown below:

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module load qiime distribution=amplicon
module load qiime distribution=metagenome
module load qiime distribution=pathogenome

The QIIME CLI can be run as shown below:

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qiime

Important usage notes:

  • Errors such as Error: QIIME 2 has no plugin/command named can be a result of not loading the correct distribution. Unload the module and load the correct distribution.
  • qiime tools view is not supported. Use qiime tools extract and then open the results with a browser.

For example:

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 qiime tools extract --input-path demux-single-end.qzv --output-path extract
 firefox extract/47e44d5e-812a-46b8-96a8-f382b5ef7e0e/data/index.html

Read the output from qiime tools extract and adjust the path accordingly. A different output path can be used.

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

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qiime_shell

Performance notes

No performance notes available

No recommended resources available

Benchmarks

No benchmarks available.

Community guides and tutorials

  • No community guides available.

Official site and documentation

Licensing information

QIIME 2 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