Analysis Guides

Qiita now uses QIIME2 plugins for analysis.

Thanks to this, we’ve got new layout of the analysis panel and the following new features:

Analysis workflow

Each analysis out of taxa summary, alpha diversity and beta diversity produces a QIIME2 visualization which can be browsed within Qiita, as well as downloadable result files. Filtering samples and rarefaction produce downloadable BIOM artifacts.

  • creating new analysis
    Select Analysis -> Create new analysis from the main Qiita toolbar. From the list of your studies, select which studies and artifacts you want to add to your analysis.
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The analysis workflow now has a similar layout to sample processing. By selecting artifacts and commands from the drop-down menu below the workflow visualization, an entire analysis workflow can be created.

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  • filtering samples

    BIOM artifact can be filtered to include samples containing specific metadata categories, or minimum/maximum frequency or number of features.

  • rarefying

    BIOM artifact can be rarefied to a desired sampling depth and results in a new rarefied BIOM artifact.

  • taxa summary

    Takes BIOM artifact as input and returns an interactive stacked barchart which can be investigated on different taxonomic levels, as well as using metadata categories.

  • alpha diversity

    Takes BIOM artifact as input. Produces a vector of alpha diversity results (text file) and downloadable interactive boxplots. Visualizations can be investigated using metadata categories and appropriate statistics are generated for all groups and pairwise.

  • beta diversity

    Beta diversity analysis on a BIOM artifact can be performed using a variety of phylogenetic and non-phylogenetic distance metrics. Produces a distance matrix as output.

  • principal coordinate analysis

    Takes beta diversity distance matrix (result of beta diversity) and generates an interactive EMPeror plot.