Analysing PacBio sequencing data with SMRT Portal on the GVL


#1

This tutorial will cover:

  • Installing SMRT Portal
  • Setting up SMRT Portal accounts
  • Uploading and importing PacBio sequencing data
  • Starting an analysis

This process is quite RAM and CPU intensive, so a climb.group sized instance is recommended for running SMRT Portal.


1. INSTALLING SMRT PORTAL

Browse to your GVL homepage by following the link from Bryn and click the Admin link at the top of the page.

Find the SMRT Portal section and click install.

This process takes a couple of minutes, and you can view progress on the homepage of your GVL instance. Wait for the green tick.

Follow the link to the SMRT Portal webpage.


2. SETTING UP SMRT PORTAL ACCOUNTS

Click Register in the top right corner and create an account for the user “administrator”. This will be automatically accepted.

After creating the “administrator” account, log off and create a user account.

Now log back in with the “administrator” account, click “admin” at the top of the page. Find the user account that you’ve just created, select it and click edit at the bottom of the screen. Set the options as below and click OK.

Finally, log out of the administrator account and log in to your newly-approved “scientist” account.


3a. UPLOADING PACBIO SEQUENCING DATA

Installing SMRT Portal creates a new user: smrtanalysis. Their home directory is /mnt/galaxy/home/smrtanalysis. This is a good place to put PacBio experiment data and consider creating and mounting a new volume if you have a large amount of it.

Often, you will download data from a url provided by a sequencing centre using wget or curl. You can get this to the right place by accessing your instance with the ubuntu user via SSH, then running:

sudo su smrtanalysis

to become the smrtanalysis user.

You will log in to /mnt/galaxy/home/smrtanalysis (check with pwd), where you can run a curl or wget to download files from a sequencing centre.

If you have your sequencing output files locally, you will need to follow a different process to upload your data (tutorial incoming).

NOTE: SMRT Portal is picky about detecting files. They must follow the correct directory structure and have a metadata.xml file present.


3b. IMPORTING PACBIO SEQUENCING DATA

Once your reads are in the /mnt/galaxy/home/smrtanalysis directory, you can import them into SMRT Portal.

Click “Import and Manage” on the SMRT Portal homepage.

Then select “Import SMRT Cells”, click the “Add…” button at the bottom of the page, add /mnt/galaxy/home/smrtanalysis to the box and Click OK.

Now select the new folder and click “Scan” at the bottom of the page. Ignore the warning and see that your data has been discovered. If it hasn’t, check the directory structure!


4. STARTING AN ANALYSIS

Return to the SMRT Portal home page and click “Create New”.

Give your job a name, and select the protocol you want to use (RS_HGAP_Assembly.3 is de novo assembly). Using the arrows in the middle of the screen, move the SMRT cell to the right pane.

Then click Save, and then Start.


Assembly stuck in the SMRT portal
SMRTportal access