Run the Mercury Variant-Calling Pipeline on Your Own Data

HGSC Baylor College of MedicineMercury, designed by the Human Genome Sequencing Center at Baylor College of Medicine (HGSC), is used as the core variant-calling pipeline for the CHARGE consortium. The Mercury pipeline is a semi-automated and modular set of tools for the analysis of NGS data in clinically focused studies. HGSC designed the pipeline to identify mutations from genomic data, setting the stage for determining the significance of these mutations as a cause of serious disease.

Thanks to HGSC’s work with us, the Mercury pipeline is now freely available to any DNAnexus user. The Mercury pipeline is located in the applets folder of the  HGSC_Mercury project. You can find the project, along with everything you need to run the applet, under the ‘Featured Projects’ section on your home page.  Login to DNAnexus or create an account today to get started immediately.

Inside the Mercury Project

  • Both whole genome and exome samples
  • All annotation and reference data required
  • Pre–configured workflow (just drag & drop your inputs)

Results from the Mercury pipeline will be made up of a set of annotated variants from your data sample. You’ll also see all of the biologically significant data that applies to the variants from the Baylor College of Medicine database, using their Cassandra annotation tool. You can easily visualize the mappings and variant calls within our integrated genome browser.

News: DNAnexus Offers Service for Clinical Testing Labs

This week we’re pleased to announce the launch of our specialized platform-as-a-service (PaaS) for the next-generation sequencing-based diagnostics market.

What does that mean? With this service, we are focusing specifically on clinical enterprises that want to eliminate the common costs and challenges associated with building clinically compliant pipelines for next-generation sequencing data analysis.

As demand for genomic data in the clinic ramps up, diagnostics companies that have traditionally used on-premise solutions are facing increasing challenges to scale their resources while meeting HIPAA and other regulatory requirements.

Clinical testing labs that are reconsidering those on-premise data centers need more than just a cloud provider; they also need a partner with expertise in genomics and bioinformatics to help build reliable, robust pipelines. That’s where we come in: with this PaaS, DNAnexus offers all of our usual rock-solid cloud computing along with access to our team of expert scientists and engineers who know this field inside and out.

Through our PaaS, clinical testing labs will be able to scale up their enterprise infrastructures for analyzing and managing DNA data. We provide a configurable API-based platform that allows users to move their analysis pipelines into the cloud, where they can utilize their own algorithms as well as industry-recognized tools and resources to create customized workflows in a secure and compliant environment.

One of our early clinical adopters, cancer researcher Boris Bastian from the University of California, San Francisco School of Medicine, said in a statement: “Working with the DNAnexus team has been invaluable for us as we deploy our data analysis pipeline to the cloud and work toward a production-grade clinical test. The DNAnexus platform is well-suited for rapid pipeline development and enterprise-readiness. We have relied heavily on their expertise in cloud-based solutions and benefited from their experience in managing data in a clinically appropriate manner.”

As part of this offering, we have ensured that our platform meets HIPAA, CLIA, and many other regulatory requirements for users working with sensitive medical information.

 

Just Launched: The DNAnexus Developer Program

Join a dynamic app incubator community!

Software Development KitCalling all bioinformaticians, computational scientists and hackers! DNAnexus, a company leveraging cloud computing to facilitate the analysis of extremely large biological data sets, has kicked off an app developer program and is looking to add novel genomics tools for users of our new platform.

Genomic data is the next frontier in truly challenging, Big Data problems. Our platform is designed to help scientists collaborate and analyze DNA data within a secure, web-based environment. Users will be able to upload or build workflows and project pipelines, choosing from their own tools, DNAnexus-provided apps, and now apps contributed by external developers like you.

Why should you care?

Uploading your app to the DNAnexus platform offers lots of advantages:

  • The DNAnexus platform is the most flexible and configurable API-based infrastructure for enabling genomic data analysis and data sharing.
  • The DNAnexus platform accepts DNA data from any sequencing instrument, so you can write for multiple sequencers and gain users among a much broader audience than a vendor-specific environment.
  • Join early and incur no out-of-pocket expenses for developing and testing your app. Receive a $1,000 credit toward cloud storage and compute resources.
  • Get recognition! We’ll be profiling our best-contributed apps and the genius developers behind them as we roll out the platform.
  • Easily showcase your app and its functionality on behemoth data sets.
  • Working with DNAnexus is easy and we are more than happy to provide free technical support while you are developing your app.
  • DNAnexus is building in monetization opportunities, so as the platform comes out of beta your app can create a flow of income.

Join Today!genomics hackers

Interested in learning more? Email developers@dnanexus.com with questions. Send the following information to join the program:

1. Your name and institution
2. Briefly explain the problem you aim to solve
3. Describe the genomics tool you plan to build