NGS data analysis, storage, and collaboration made easy Welcome to push-button informatics

BaseSpace Cloud and Onsite Bioinformatics

BaseSpace is Illumina's genomics computing environment for next-generation sequencing (NGS) data analysis and management. This flexible solution is available as both a cloud and onsite bioinformatics solution. Now sequencing labs can easily and securely analyze, archive, 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 from any Illumina instrument from the BaseSpace website, thereby experiencing a full sample to answer solution.

BaseSpace can be accessed via an intuitive web-based GUI, or a Linux-based command line interface.

*BaseSpace Onsite currently does not support HiSeq X.

BaseSpace Platform Features

Key features of BaseSpace, besides NGS data analysis, sample/run management, and cloud bioinformatics or onsite options, include:

  • Sequencing instrument integration: BaseSpace 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 solves NGS data storage and management challenges with practically inexhaustible storage space, whether cloud or onsite.
  • Easy data sharing: Because the BaseSpace cloud and onsite bioinformatics solutions are 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 offers an intuitive, easy-to-use web-based interface for managing your data. For those more comfortable with a Unix interface, BaseSpace offers a command line option for navigation, downloads/uploads, launching analysis (including automatic launch of applications) as BaseMount.

Learn More about BaseSpace Platform Features

NGS Data Analysis in the Cloud or Onsite with BaseSpace Apps

BaseSpace offers a wide variety of NGS data analysis apps (tools). These include:

  • 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 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

In addition to these publicly available Apps, users can run their own bioinformatics pipeline on BaseSpace as a private App.

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), de novo assembly, and 16S metagenomics.

Learn More about BaseSpace Apps

NGS Sample and Run Management
with BaseSpace Prep

BaseSpace makes sample and run management easy using the Prep tab feature, an intuitive, graphical environment for one-stop library and run preparation.

  • Prepare and manage biological samples, libraries, pools and planned sequencing runs directly in BaseSpace
  • Easily start sequencing runs through seamless integration with the NextSeq 500 System
  • Import biological samples or library information in batch mode for large experiments

The BaseSpace Prep tab also supports NeoPrep, Illumina’s automated library preparation solution.

Learn More about BaseSpace Prep

BaseSpace Onsite

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

Learn More about BaseSpace Onsite

BaseSpace Developer Resources

Create your own bioinformatics app on BaseSpace with our step-by-step instructions. Learn about upcoming developer conferences.

Access BaseSpace Developer Resources

Additional Resources

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

Getting Started with BaseSpace View Video Learn how to get started with push-button bioinformatics in BaseSpace.

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

BaseSpace Apps Quick Guide View PDF

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