BaseSpace Hub NGS Data Analysis (2024)

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Integrate, analyze, and discover with BaseSpace Sequence Hub

BaseSpace Sequence Hub is the Illumina cloud-based genomics computing environment for next-generation sequencing (NGS) data management and analysis. Sequencing labs can store and share sequencing data, and researchers can simplify and accelerate NGS data analysis with push-button tools. Labs can also set-up and monitor their sequencing runs in real time on any Illumina instrument. BaseSpace Sequence Hub can be accessed via an intuitive web-based interface or Linux-based command line tool. For customers who need a local solution, we offer BaseSpace Onsite Sequence Hub.

BaseSpace Hub NGS Data Analysis (1)

Register now for a BaseSpace Sequence Hub Basic
account, which includes 1 TB Storage.


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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.




StorageUp to 1 TB11 TB plus pay as you go1 TB plus pay as you go
Compute30 Day Free Trial2 of 250 complimentaryCredits3250 complimentaryiCredits3 plus pay as you go250 complimentaryiCredits3 plus pay as you go
Premier Data Security and Privacy
Run Setup
Unlimited Monitoring
Unlimited Sharing4
AppsFree apps only
(after trial period expires)
Comprehensive Security Framework
Multi-user Access
Bioinformatics Professional Services Support5 (8 hours)
(24 hours)
Multiple Workgroups
Private Domain and Single Sign-on
Supports customers in a HIPAA regulated environment
Access Control & Audit
PriceFreeContact a Sales RepContact 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 BaseSpace Hub NGS Data Analysis (2)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.

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