For most QIIME analyses, you'll want to use the Greengenes Core Set files. To get these, first open a new terminal window (click on the black box with a > symbol on the top of your screen).

Ensure that you are in your home directory by entering the command:

cd

Then, run the two commands:

wget http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/core_set_aligned.fasta.imputed

wget http://greengenes.lbl.gov/Download/Sequence_Data/lanemask_in_1s_and_0s

Note that the command wget works as follows: "wget URL_to_file". The entire command is one line.

This will download the two required files to your home directory. These files are used by QIIME and their location is set in the /home/qiime/.qiime_config file, if you move them from your home directory, please, update this file with the new location.

Once you have downloaded these files, you should be ready to run your first QIIME analysis. The best way to start is reading the tutorial, available locally by double clicking on the documentation.html in the Before_you_start folder. If you are using the current Virtual Machine version you can also use the online documetation, here:
   http://www.qiime.org/
