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About Graph Genome apps

Overview of graph technology

A linear reference genome is not not an accurate description of genetic variants within a population because it is built from a small number of individuals. This leads to inaccurate read alignment against that reference, which in turn biases the discovery of new genetic variants.

This reference bias can be addressed by using a graph structure to achieve a more complete description of genetic variation within a population. Work with small genomic regions containing high sequence or structural diversity has shown that using a graph reference produces better read alignment and improved variant calling.

Through applying graph technology at the whole genome level, the Seven Bridges Graph Genome Apps enable highly accurate read alignment and somatic variant calling for cancer research applications.

The graph reference genome

The graph reference genome is built using genomes from a wide range of human populations, including data from the 1000 Genomes Project and the Simons Genome Diversity Project Datasets. The differences between genomes are stored for every position in the genome using a directed acyclic graph. Given that human genomes are 99.9% identical, the increase in storage requirements is minimal with the addition of a new genome to the population reference graph, allowing analysis to be carried out at a previously impossible scale.

Graph Genome Apps

  • Graph WGS: Graph-based whole genome sequencing analysis
  • Other graph-based apps will be available soon!

Access to Graph Genome apps

You need a Seven Bridges Platform account to be able to access Graph Genome apps.

Get in touch if you would like to run Graph Genome apps:

  1. Click Public Apps (top menu bar) once you are logged into your Seven Bridges Platform account.
  2. Type "graph" into the search box to find the Seven Bridges Graph Genome apps. They are marked with a .
  3. Click on the Graph Genome app you are interested in using. This will take you to the app page.
  4. Click Get in touch in the box beneath the app title.
  5. In the popup, please give some details about why you are interested in using the app.
  6. Click Send request.
  7. Seven Bridges will be in touch shortly with a response.

Once you get access to the Graph Genome app, the Run and Copy buttons will become available, enabling you to use the app on the Seven Bridges Platform.

Payment

When you run Graph Genome apps on the Seven Bridges Platform, you will be charged per execution. For example, performing a whole genome sequencing analysis using two high quality paired-end raw FASTQ files (~80 GB) – similar to the task described in the Graph WGS tutorial – will cost you about $15.88.

Particularities of Graph Genome apps

  • Access: You need specific access to run each of the Graph Genome apps. Being part of a project containing a Graph Genome app does not automatically allow you to run the app. Please get in touch if you would like to use one of the Seven Bridges Graph Genome apps.
  • As part of a workflow: Graph Genome apps are standalone and cannot be connected to other tools or workflows using the Workflow Editor.
  • On Google Cloud Platform: Graph Genome apps are only available on the Seven Bridges Platform version using the AWS cloud infrastructure. If you are using the Seven Bridges Platform with the Google Cloud Platform infrastructure, please get in touch with us at support@sbgenomics.com to get access to Graph Genome apps.
  • Troubleshooting: If your task running a Graph Genome app fails, the error is immediately analysed and you will shortly be contacted by one of the Seven Bridges bioinformaticians with advice on how to get the task up and running.
  • Task logs: As a Graph Genome app user, you do not have access to the corresponding task logs. However, if your task does fail, one of the Seven Bridges bioinformaticians will be in touch to help with troubleshooting.
  • Accessing the CWL JSON file: As a Graph Genome app user, you do not have access to the Common Workflow Language (CWL) JSON file for the app. If you request the CWL JSON for a Graph app via the API, a limited number of fields will be returned.
  • Accessing the Docker image: Users don't have access to the Docker images for Graph Genome apps.
  • Editing Graph Genome Apps: Users cannot edit the Graph Genome apps or see any of its components.

About Graph Genome apps