[LEGACY] Tutorial

This tutorial walks you through using the Seven Bridges graph-based whole genome sequencing app (Graph WGS) to generate alignment and variant information for the NA12878 reference cell line using raw paired-end Illumina sequencing data.

Prerequisites

Everything you need to carry out this tutorial is available on the Seven Bridges Platform. Before you start, make sure you have:

• An account on the Seven Bridges Platform using the Amazon Web Services cloud infrastructure
• Access to Graph WGS

The Seven Bridges Platform runs on both Amazon Web Services (AWS) and Google Cloud Platform (GCP) cloud infrastructures. If you signed up after early 2016, you will have had the option to choose between AWS and GCP as your cloud provider. Graph WGS is only available through the Platform running on the AWS cloud infrastructure.

Outline

As with any analysis on the Platform, the steps of running Graph WGS involve setting up your project, running your task, and getting your results:

Set up your project

1. Create a new project

   a. From your Seven Bridges Platform Dashboard, create a new project called "graph-tutorial". Select Projects from the top navigation, and click Create a project
   b. Name your project "graph-tutorial" in the popup that comes up
   c. Click Create to finish. This takes you to the project dashboard. All information related to this project is organised into tabs containing files, apps (tools and workflows), tasks (app executions), and project members.

2. Add files to your project

   a. Navigate to the Files tab within the project you just created
   b. Click +Add files
   c. Select Public files from the top of the left hand side menu
   d. Type "NA12878" into the search box
   e. Select "NA12878-Garvan-Vial1_R1.fastq.gz" and "NA12878-Garvan-Vial1_R2.fastq.gz". They should be the top two results.
   f. Click Copy to Project. You don't need to add any tags for the files, just click OK to finish
   g. Close the Add Files window. This takes you to the Files tab in your "graph-tutorial" project, which now contains the two files you've just added.
   Note that the FASTQ files used in this tutorial already contain the metadata required to run Graph WGS.

3. Add Graph WGS to your project

   a. Navigate to the Apps tab within your "graph-tutorial" project
   b. Click +Add app. This brings you to the Public Apps tab of the Add apps window.
   c. Start typing "Graph-based whole genome sequencing analysis" into the search box.
   d. Click Copy on the app card to copy the app to the project you're in.
   e. Click Copy again to confirm the app URL.
   f. Close the Add apps window. This takes you back to the Apps tab, which now contains the "Graph-based whole genome sequencing analysis" app.

Run Graph WGS

1. Create a draft task

   a. Make sure you are on the Apps tab in your "graph-tutorial" project
   b. Click , found under Actions for the Graph WGS app you just copied. This creates the draft task and also takes you to the draft task page, as emphasized by the label next to the title. This is the page where you set up your analysis. Initially you will see some red input data parameter errors because you haven't set the input parameters yet. We'll do that next.

2. Set your inputs

   a. Click the Set Input Data tab of the draft task page
   b. Select Sample from the Batch by dropdown menu
   c. Click Pick file(s)
   d. Select the two FASTQ files you added earlier from the window that comes up ("NA12878-Garvan-Vial1_R1.fastq.gz" and "NA12878-Garvan-Vial1_R2.fastq.gz")
   e. Click Select to add the files to your draft task.
   f. Click the Define App Settings tab on the draft task page
   g. Select "GRCh v37 (recommended)" from the drop-down menu. This selects the version of the graph reference genome to be used for your analysis.

3. Run your task

   a. Click Run.
   b. It should take around 8 hours for the task to complete

Get your results

You can follow the progress of your task on the Tasks tab and you will also receive an e-mail notification when the task is finished. Running this task should take around 8 hours.

Clicking the task name will take you to the task page detailing the inputs, the app settings and the outputs the task has produced. Your results can be found under Outputs:

• BAM file: contains read alignment information
• VCF file: contains all the variants detected by Graph WGS

View the alignment in the Genome Browser

1. Click on your output BAM file on the completed task page
2. Scroll to the bottom of the resulting page to see the alignment in the Genome Browser

Use outputs in other projects on the Seven Bridges Platform

1. Go to the Files tab on your project dashboard
2. Select your output files, "alignment.BAM" and "variants.VCF", in this case
3. Click Copy to and then the name of the project you want to use the files in from the dropdown menu
4. Click OK in the popup to start copying the files

Download files

1. Go to the Files tab on your project dashboard
2. Select the files you would like to download
3. Click the Download button above the list of files and follow the instructions from your browser

Get download links

1. Go to the Files tab on your project dashboard
2. Select the files you would like to download
3. Click the arrow next to the Download button and select Get download links
4. In the popup, you can either copy the links to your clipboard or save them to a TXT file

📘

We're here to help you use Graph WGS on the Seven Bridges Platform.

If you can't find what you are looking for in the documentation, please get in touch with us at [email protected].