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Integrate, analyze, and discover with BaseSpace Sequence Hub

Solving All Your Bioinformatics Needs

BaseSpace Sequence Hub Subscription Tiers

BaseSpace Sequence Hub subscription tiers enable labs of all sizes to achieve maximum efficiency with tight instrument integration and simplified collaboration. We have three tiers of offerings.





Storage Up to 1 TB1 1 TB plus pay as you go 1 TB plus pay as you go
Compute 30 Day Free Trial2 of 250 complimentary Credits3 250 complimentary iCredits3 plus pay as you go 250 complimentary iCredits3 plus pay as you go
Premier Data Security and Privacy      
Run Setup      
Unlimited Monitoring      
Unlimited Sharing   4    
Apps Free apps only
(after trial period expires)
All All
Comprehensive Security Framework      
Multi-user Access      
Bioinformatics Professional Services Support     5 (8 hours)
(24 hours)
Multiple Workgroups      
Private Domain and Single Sign-on      
Supports customers in a HIPAA regulated environment      
Access Control & Audit      
Price Free Contact a Sales Rep Contact a Sales Rep

1. Customers wanting to purchase additional storage must upgrade to Professional or Enterprise account
2. Customers wanting additional iCredits must upgrade to a Professional or Enterprise account
3. iCredits will be applied to users account upon launch of Compute Billing
4. Unlimited sharing and transfer apply only to Basic accounts under the 1 Tb storage quota.
5. Professional services are not included with the academic plans.
For Research Use Only. Not for use in diagnostic procedures.

Simplifying Bioinformatics to Speed Up Discovery

BaseSpace Sequence Hub is the only bioinformatics platform that is directly connected to all Illumina sequencing instruments*.

Stream sequencing runs and store data immediately.

  • With unlimited storage on the cloud, you never have to worry about running out of space**.
  • Monitor sequencing runs in BaseSpace Sequence Hub with Sequencing Analysis Viewer (SAV) charts.
  • Perform routine data analysis immediately with the push of a button.
  • Choose from more than 70 pre-packaged analysis options available from Illumina and third-party developers
  • Open platform allows you to upload your own pipeline as a public or private app

With BaseSpace Sequence Hub there is no need to set-up and maintain IT infrastructure to store and analyze your genomics data.

We offer scientific and technical consulting through our Services offering to help guide you through bioinformatics workflows. Bioinformatics Professional Services offers group and one-on-one sessions on topics including introduction to bioinformatics, how to use various BaseSpace Sequence Hub features to maximize productivity, in-depth discussions on specific NGS workflows, and assistance creating custom pipelines into BaseSpace Sequence Hub.

*HiSeqX does not connect to BaseSpace Onsite Sequence Hub
** Customers wanting to purchase additional storage must upgrade to Professional or Enterprise account

Explore the Benefits of BaseSpace Sequence Hub

See how our informatics platform offers a rapid, scalable, and secure NGS solution with minimal infrastructure investment.

View Infographic

Key Features

In addition to NGS data analysis, sample/run management, and cloud bioinformatics or onsite options, key features of BaseSpace Sequence Hub include:

  • Sequencing instrument integration: BaseSpace Sequence Hub is directly integrated with Illumina sequencing instruments. This integration streamlines real-time run monitoring and QC, and facilitates data sharing and transfer.
  • Simplified NGS data management and storage: BaseSpace Sequence Hub solves NGS data storage and management challenges with practically inexhaustible storage space in the cloud*.
  • Easy data sharing: Because the BaseSpace Sequence Hub cloud is accessible everywhere, data sharing is instantaneous. Easily share individual sequencing runs or entire projects with collaborators anywhere in the world with a few clicks.
  • Multiple user Interfaces: BaseSpace Sequence Hub offers an intuitive, easy-to-use web-based interface for managing your data. For those more comfortable with a command line interface, BaseSpace Command Line Interface and BaseMount enable navigation, download/upload, launching analyses (including automatic launch of applications) and enhanced automation.
  • Sample and Run Prep: The Prep tab is an intuitive, graphical environment for one-stop library and run preparation.

Learn More about BaseSpace Sequence Hub Features

* Customers wanting to purchase additional storage must upgrade to Professional or Enterprise account.

NGS Data Analysis Apps

BaseSpace Sequence Hub offers a wide variety of powerful NGS data analysis apps, including:

  • Illumina Core Apps: Developed or optimized and fully supported by Illumina
  • BaseSpace Lab Apps: Developed using an accelerated process to make them available to BaseSpace Sequence Hub users faster than conventional Illumina Apps, and provided as-is
  • Third-party apps: Developed and supported by a thriving ecosystem of third-party app providers in BaseSpace Sequence Hub

In addition, BaseSpace Sequence Hub enables users to develop custom bioinformatics apps in BaseSpace Sequence Hub. App developers are able to keep apps private, share with collaborators, or submit for publication.

Together, these apps cover the common data analysis methods used with Illumina sequencing data. These methods include RNA-Seq, exome /enrichment, amplicon, whole-genome sequencing (WGS), amplicon, de novo assembly, 16S metagenomics, and more.

Learn More about BaseSpace Apps

BaseSpace Onsite Sequence Hub

BaseSpace Onsite Sequence Hub is a local version of the BaseSpace Sequence Hub cloud bioinformatics solution that enables you to safely and securely store, share, and analyze NGS data from MiniSeq, MiSeq, MiSeqDx (in RUO mode), NextSeq 500, NextSeq 550, HiSeq 2500, HiSeq 3000, and HiSeq 4000 systems. 

Learn More about BaseSpace Onsite Sequence Hub

Additional Resources

BaseSpace Sequence Hub Data Sheet View PDF Learn more about BaseSpace Sequence Hub highlights, tools, and applications.

Introduction to BaseSpace Sequence Hub View Video Learn how you can store and analyze your genomic research with ease, and effortlessly manage all of your sequencing runs.

Monitoring Instrument Performance View PDF BaseSpace Sequence Hub enables users to submit sequencing instrument operational data, so Illumina can monitor instrument performance and resolve unforeseen issues.

BaseSpace Sequence Hub White Paper View PDFBaseSpace Sequence Hub has a set of comprehensive policies and controls for data security and privacy.

BaseSpace Onsite Sequence Hub View Video BaseSpace Onsite Sequence Hub allows users to access their next-generation sequencing data anywhere.

BaseSpace Apps Quick Guide View PDF

BaseSpace Sequence Hub Support Find user guides, app release notes, and additional technical information. Access BaseSpace Sequence Hub Support

Immuno-oncology Informatics Apps Guide View PDF Informatics tools enable discovery and analysis with standard Illumina sequencing applications.

BaseSpace Sequence Hub is intended for research applications and not for any diagnostic or clinical use. It is intended to be used with Illumina research products only.