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Enhancements to Run Monitoring

We’ve recently added some improvements to the Sequencing Runs list. These updates should help to quickly get basic quality information about each run, without needing to click into Run details pages.

For example, % reads passed filter (%PF), average %Q30, yield, and cycles (for Read1 and Read2) are now columns on the Runs list.

Run Quality Metrics

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New RNA-Seq Alignment App with support for TruSight RNA Pan-Cancer and more

With the launch of the TruSight RNA Pan-Cancer panel, a targeted enrichment panel for the detection of variants, fusions, and gene expression profiles in 1385 cancer-associated genes, Illumina is pleased to provide an intuitive BaseSpace App, RNA-Seq Alignment v 1.0, that supports simple push button analysis of the data.


RNA-Seq Alignment

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Announcing File Upload with BaseMount

We are pleased to announce a new release of BaseMount, our FUSE driver to mount your BaseSpace account as a Linux filesystem.

BaseMount allows you to navigate on the command line through projects, samples, runs and app results, and interact directly with the associated files exactly as you would with any other local file system.

BaseMount allows you to download – and now upload – files, but maybe more importantly, it allows you to work interactively with your files stored on BaseSpace without having to download them. You may, for example, run samtools directly on a large BAM file, and it will only fetch the blocks needed for your query.

This update (BaseMount v0.12) includes:

  • Write-mode: project and appresult creation, file upload
  • Properties can be viewed and edited
  • Improved documentation
  • Relaxed timeout for low bandwidth
  • Unmount assistance, listing blocking processes and offering lazy-unmount

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Introducing BaseSpace Professional!

The BaseSpace team is excited to introduce the BaseSpace Professional tier, which enables access to a host of new features and services, including:

  • Multi-user access with Workgroups
  • 8 hours of Bioinformatics Professional Services from Illumina
  • Expandable storage and compute credits

With BaseSpace Professional we are releasing a new Workgroup feature to enable seamless and efficient data sharing for you and your colleagues. Workgroups enable collaboration on a global scale.

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Introducing BaseSpaceCLI

In July, we released an early-access version of BaseMount, a command-line tool to allow you to navigate your BaseSpace account and work with your files on-demand.

To complement this browsing capability, we are adding to the suite of BaseSpace Command Line Tools by releasing the BaseSpaceCLI (Command Line Interface). BaseSpaceCLI provides two new areas of functionality, uploading samples and launching apps, but also comes with a host of other commands to help you work with your BaseSpace data and apps.

BaseSpace Command Line Tools

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New BaseSpace Features and Tiers

[Updated on January 19th, 2016]

We launched BaseSpace in 2011 with a commitment towards ‘simplifying the informatics experience‘, and we have delivered via frequent feature releases, feature improvements, and a growing ecosystem of informatics Applications (Apps). Currently we have more than 60 BaseSpace Apps covering a wide range of bioinformatics analysis needs from alignment and variant calling to metagenomics, and even proteomics. Users can also run their own analysis pipelines on BaseSpace as private Apps. With the recent NeoPrep integration, users can set up a library prep, monitor sequencing while uploading data directly from the instrument, and analyze the data for a truly end-to-end experience, all within the secure BaseSpace cloud environment.

In the last several years, Illumina has continued to innovate, expanding its sequencing systems portfolio to offer a wide range of solutions from the focused power of the MiSeq to the population power of the HiSeq X. The rapidly growing adoption of these systems and their varied applications have resulted in increasingly diverse customers needs in terms of bioinformatics support. To serve these diverse needs, we are excited to announce the addition of a number of new features to the BaseSpace platform. These features have been packaged into two new subscription levels based on use cases: Professional and Enterprise.

The basic BaseSpace account will be available for free, and will include 1TB storage space. With the basic subscription, users can monitor sequencing runs, stream sequencing data directly to the cloud, store and share data, and access all Apps. The early access Linux-based command line interface, BaseMount, will continue to be available as well.

BaseSpace Professional includes these basic features and adds the convenience of multi-user account access. This feature allows multiple personnel within labs, organizations, consortium etc to access a common account with their individual logins.  Subscriptions will include license for unlimited number of users.

BaseSpace Enterprise adds functionalities useful for larger organizations: subscribers will get their own BaseSpace domain with up to 25 users (and option to add more), single-sign on using institutional credentials, and the capability to form groups within the domain. This level also supports features such as fleet monitoring (ability to monitor multiple instruments and statistical information on sequencing runs over time), and the ability to integrate BaseSpace with LIMS (to be available later).

Both Professional and Enterprise subscriptions will include support to help NGS users with questions regarding genomic analysis and bioinformatics workflows. The Professional and Enterprise subscriptions will be available in early 2016 and additional details on pricing and ordering process will be provided soon.

BaseSpace users at Professional and above will be able to purchase additional storage (over the 1TB limit) as annual subscriptions in multiples of 1TB. Storage will be charged at Amazon Web Service (AWS) retail prices (currently $360/TB/yr for storage under 50TB).

Computation for running Apps on BaseSpace will be offered free to all users till March 2016*. Subsequently, computation will be available for purchase at AWS retail rates, Both new and existing customers will receive an introductory $250 in computation credit for trying out various Apps.

Please note that this announcement will have no immediate effect on the users of BaseSpace. Users will continue to have access to all current features and storage. Users will soon receive an e-mail with details about storage and account upgrade options.

We thank the ever-growing community of BaseSpace users for their support and look forward to rolling out new these features, as well as more Apps. Stay tuned!


*Subscription charges for paid Third-party Apps will apply.

VCAT 2.3 with Haplotype Compare and FASTQ Toolkit 2.0

In January 2015, Illumina introduced the VCAT 2.0 BaseSpace app and the associated Platinum Genomes v7 truth data set. Now we are happy to announce an upgraded Variant Calling Assessment Tool (VCAT 2.3,, which has integrated access to the open source Haplotype Compare tool, in addition to the legacy VCF-Tools based assessment engine. We also updated the truth data sets with Platinum Genomes v8. Read More…