$ sudo apt-get remove qiime 

Uninstall qiime including dependent package

If you would like to remove qiime and it's dependent packages which are no longer needed from Ubuntu,

$ sudo apt-get remove --auto-remove qiime 

Use Purging qiime

If you use with purge options to qiime package all the configuration and dependent packages will be removed.

$ sudo apt-get purge qiime 

If you use purge options along with auto remove, will be removed everything regarding the package, It's really useful when you want to reinstall again.

$ sudo apt-get purge --auto-remove qiime 

See Also,