Introducing Amazon Omics
Are you interested in learning more about the new Amazon Omics platform? Amazon recently introduced its Omics platform, a purpose-built service to store, query, and analyze genomic and biological data at scale. Bioinformatics analysis platforms like Amazon Omics allow researchers to bring genomic, transcriptomic, and other omics data together to generate insights to improve human health and advance scientific discoveries.
The market for bioinformatics analysis platforms ranges from one-size-fits-all interfaces to fully custom tools and one-on-one support. Depending on your project, different considerations will inform your choice. With Amazon’s new platform launching, it’s important to ask: how does Amazon Omics work, how much does it cost, and how does it compare to other platforms on the market?
What Are Bioinformatics Platforms?
The first main distinction lies between bioinformatics platforms (i.e. Amazon Omics, Galaxy, and more) and bioinformatics service providers (i.e. Bridge Informatics).
Bioinformatics platforms, in their current model, generally:
- Provide researchers access to bioinformatics capabilities without using the command line (via point-and-click, user-friendly interfaces)
- Have a self-service type model (though platform companies may also provide some support and services)
While the platforms share these features, they differ from each other in either the tools they have available, the data they can process, or the cost to run analysis jobs.
Bioinformatics service (BaaS) providers, on the other hand, are different in that they are comprehensive and end-to-end. BaaS providers can support their clients from raw data pre-processing to building cloud storage infrastructure and custom bioinformatics pipelines. However, BaaS providers can also support clients using existing bioinformatics platforms and tools like Galaxy and Basespace.
Overview of Current Bioinformatics Platforms
These platforms vary in their strengths and weaknesses: some may only support specific data types, or use different pricing models. Current bioinformatics platforms include:
Amazon Omics
Amazon Omics has three primary components:
- Omics-optimized object storage that helps customers store and share their data efficiently and at a low cost
- Managed compute for bioinformatics workflows that allow customers to run the exact analysis they specify, without worrying about provisioning underlying infrastructure or building their own tools
- Optimized data stores for population-scale variant analysis
Being so new to the market, there is limited feedback so far about Amazon Omics. However, the initial impressions seem to be that while it could be a useful tool for standard workflows, it remains to be determined how much you can customize a specific workflow to fit the analysis needs for certain projects.
Galaxy
Galaxy is a publicly funded, academic-developed-and-maintained platform and community meant to be deployed by individual institutions. Some Galaxy instances are publicly accessible but can be limited in the resources a user can access. Galaxy servers require someone (typically full-time) to deploy and maintain the server, which can be the main cost of this platform.
Basespace
Basespace is Illumina’s current bioinformatics workbench but is slowly being phased out by the Illumina Connected Analytics (ICA) platform. Basespace accounts are free, but users have to pre-pay for analyses rather than paying after the fact like some other platforms.
10x Genomics
The 10x Genomics Cloud Analysis platform is relatively specialized and was developed only for 10x single-cell data. It only runs cell ranger, so is quite limited in the kind of data you can analyze and how you can analyze it. However, analysis on the platform is included in the cost of a 10x Genomics kit.
DNAnexus
DNAnexus leverages AWS-based cloud computing for its three main products:
- Titan: Next-Generation Sequencing Data Analysis
- Apollo: Multi-Omics Data Science Exploration, Analysis, and Discovery
- Portals: Customized, Private, and Collaborative Environments
However, the pricing structure for DNAnexus can be a little opaque, with limited information available on their site.
SevenBridges
SevenBridges has a heavy focus on providing access and analytical tools for large, publicly-available genomic datasets. In addition, they offer similar infrastructure and bioinformatics workflow options to other bioinformatics platforms.
Google Cloud Life Sciences
Google has also introduced a beta version of a cloud-based life science omics and bioinformatics platform. They claim strengths like cost optimization, integration with existing bioinformatics platforms and tools (like Galaxy), and infrastructure as a service allowing for scalability.
Bioinformatics Support and Outsourcing
In contrast to using these existing bioinformatics platforms, you can outsource your bioinformatics analysis to a BaaS provider like Bridge Informatics. The advantages of Baas include:
- Flexibility: Providers like us can work with any data type and create customized pipelines to fit a client’s needs, including opportunities to dig into experimental design and analysis goals with clients, and work with them to make sure they are getting exactly what they need
- Different pricing structures: We offer both pay-as-you-go plans (for researchers that don’t need to analyze data frequently) or subscription-based plans (for researchers that need to process data on a regular basis)
Different pricing structures: We offer both pay-as-you-go plans (for researchers that don’t need to analyze data frequently) or subscription-based plans (for researchers that need to process data on a regular basis)
Outsourcing your bioinformatics needs to Bridge Informatics allows us to tailor data storage, workflows, and more to your specific needs. Whether a client needs a truly custom pipeline or wants support using a predefined workflow on an existing platform, Bridge Informatics can help. We can write custom pipelines, set up secure and accessible data storage, and jump into any bioinformatics platform on the market depending on what is best for your analysis needs. Book a free discovery call today to talk to our team about designing the best approach for your project needs.
Caitlin Winkler, Data Scientist, Bridge Informatics
If you’re interested in reaching out, please email [email protected] or [email protected].
