Using QIIME to analyze 16S Sequences with core_qiime_analyses

 0. Pre-requisites

Before running the tutorial example, you will need to register for access to n3phele, as outlined here

 1. Accessing the n3phele site

 To access the n3phele site, click here to open a new window for the n3phele cloud service url:
 Note that the address starts with https: rather than just http: This ensures that the communication with the site is secured using encryption. This means that no one can eavesdrop and get access to your passwords or other credentials as you enter them into n3phele during the setup process. You will see a window similar to that shown in Figure 1. Log into n3phele using the email address and password you entered during the registration process.

2.  Selecting a command to run

  After your login, you will see a list of available Commands in n3phele, similar to the display shown in Figure 2. Scroll down this list, until you see an entry called "core_qiime_analyses". Clicking on the core_qiime_analyses link will take you to the command page for that command (Figure 3). 

3.  Entering the command parameters

 To run a command in n3phele you need to fill in the relevant parameters. The core_qiime_analyses script has both required parameters (denoted by the yellow triangle until filled in) and optional parameters. In Figure 3 you can see that the input sequences and mapping file are required parameters.

 Each parameter has a description field next to it defining what should be entered. Most of affect the analysis that will be run with QIIME. Exceptions to these are in the "Execute On" section:
  1. Select EC2 as the cloud on which to run the command
  2. Enter a run identified (such as "my tutorial run")
  3. Select "Send you an email on completion" so that you will get a notification email

Pressing "Run" will boot up an Amazon EC2 instance (which will charge your account) and start the analysis.

Note: n3phele recognizes and handles zip files in a special way, for both input and output files. You can read more about this here
The command request will be submitted to n3phele and in a few seconds you will be transferred back to the Command page. In the Recent Activities column a new activity matching the name you entered at step 2 (for example "my tutorial run") will appear, which you can use to track progress of the run.

4. Watching the command progress

The progress of a particular activity can be tracked by watching the entry in the Recent Activities window. For more detail by you can click on that item to bring up details of the run (see Figure 4). See here for a further description about activity tracking. When the job is completed an email will be sent to your login email address summarizing the activity. 

Problems can sometimes occur in the runs, which may cause your run to fail. For example, Amazon instances can go down, causing your run to fail part way through. This information will be logged in your progress view.










5.  Accessing the results

When your analysis completes the results can be accessed using the "Files" menu item on the left which opens the File Browser (Figure 5). When your job completes your results will be stored here in the repository that you chose when setting the destination for your output files. To download your results you can enter the file browser and select the relevant repository. You can click on individual files to download them to your local machine.

You can also make your a result folder publicly available, for example to share with collaborators. To do this, click the 'actions' link under the folder name and choose 'make public' (Figure 6). You can then click the links in that folder (Figure 7) to open them in a new web browser tab or window. Figure 8 illustrates the index.html page that is generated by a core_qiime_analysis run.
Figure 1. n3phele login page.

Figure 2. Selecting a command.

Figure 3. core_qiime_analyses command page.

Figure 4. Progress view.

Figure 5. File browser.

Figure 6. Making data public for viewing via web.

Figure 7. Public data.

Figure 8. Viewing index of core_qiime_analyses results.