264    ◾    Bioinformatics

This will display the program usage, options, and available commands. A command can

be a QIIME2 utility tool (info, tools, dev) or QIIME2 plugins. We will use the “tools” com-

mand very often. To use a QIIME2 command or plugin, it must be in the “qiime <com-

mand>”. For instance, to use “tools” command, run the following:

(qiime2)$ qiime tools

The QIIME2 plugins are software packages developed by programmers to be used for anal-

ysis. Plugins work through two functional units: methods and visualizers. Before any data

processing, QIIME2 converts input raw data into a special format called QIIME2 artifacts.

An artifact is a compressed file with the “.qza” file extension. For the output, QIIME2

FIGURE 7.1  General QIIME2 workflow for amplicon-based sequence data analysis.