Supported Applications


  • Description

    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.

  • Primary Citation*

    J. G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello, N. Fierer, A. G. Peña, J. K. Goodrich, J. I. Gordon, G. A. Huttley, S. T. Kelley, D. Knights, J. E. Koenig, R. E. Ley, C. A. Lozupone, D. McDonald, B. D. Muegge, M. Pirrung, J. Reeder, J. R. Sevinsky, P. J. Turnbaugh, W. A. Walters, J. Widmann, T. Yatsunenko, J. Zaneveld, and K. R.. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods. Nature Publishing Group.

    • *Full citation information available through

  • Citation Note

    QIIME 2 does not yet have its own citation. Please cite the main website ( and for now please cite the original QIIME 1 publication until QIIME 2 has its own publication.