QIIME 2 is actually a collection of programs written in different languages accessible via the command line using common interfaces or plugins. There are separate plugins for each step in processing sequence data: importing data, denoising, clustering, classifying, etc. Plugins typically operate on artifacts, which are compressed archives containing data, metadata associated with the data and files giving the providence of the data. These qza files are actually zip files that can be unpacked and decompressed using unzip.
Some data artifacts can be converted to visualization artifacts have the extension qzv. To visualize the contents of qzv file, load it into the box at the top of the page at https://view.qiime2.org/.
For instructions on how to use a particular plugin, go to the QIIME 2 help page for your version of QIIME2 and click on “plugins” in the menu on the left side of the page. On the page that opens, click on the plugin that you wish to use and then “Methods.” This will take you to a page giving the type of input and output for the plugin along with all of the options to use with the plugin.
Somewhat curiously, the plugins for importing data are not among the plugins listed on the help page. Instead methods for importing data are given about half way down the tutorial page under “Importing data.” In most cases you will want to use one of the fastq manifest methods to import your raw sequence data. There are separate methods for importing paired-end and single read data; both allow associating the file names with a sample name.
All of this will become clearer as you work through the exercises listed in the menu on the right of this page. All of the tutorials use small data sets so that they are easily and quickly run on a notebook computer.