New BaseSpace Features and Tiers

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. In addition, the Professional tier includes automatic launch of applications, and full use of a command line interface. Subscriptions will include license for up to 5 users, with the option to add additional 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.

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 any tier 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 $200 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. The 1TB storage limit will not be implemented till January 2016, and 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.

New and Updated Illumina Core Apps

Since our last app news in August and September, we’ve published more than 15 new and updated apps in BaseSpace! Let’s explore five of those:


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Interpret Protein-Coding and Splicing Variants with MutationForecaster

We are pleased to announce the release of the MutationForecaster v2.0 App in BaseSpace.

MutationForecaster is a suite of tools created by Cytognomix geared to provide researchers with a single interface for genomic variant analysis and validation. The App interprets both protein coding and splicing variants, its strength is in providing the most robust mRNA splicing analysis on the market, presenting three tools created by Cytognomix specifically for this purpose:

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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…

BaseMount: Directly Linking NGS Data to R Packages for RNA-Seq Differential Expression Analyses

With the recent launch of BaseMount, access to your NGS data has never been so convenient. This early access release is available for all Linux-based operating systems and utilizes a command line interface (CLI) to access personal Projects, Samples, Runs, and AppResults within your BaseSpace account. Below are some simple steps to effectively transform your RNA-Seq data straight from our very own RNA Express app into a Normalized Count Plot, MA-plot, and Principal Component Analysis (PCA) plot. We are going to be using the popular Bioconductor DESeq2 package to construct the plots and the example is a differential expression analysis comparing two tissue samples: Human Brain Reference RNA (HBRR) and Universal Human Reference RNA (UHRR). Follow these steps below to get started:

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Differential Methylation Analysis with the MethylKit BaseSpace Labs App

In May 2015, Illumina introduced the MethylSeq 1.0 BaseSpace app for performing analysis on bisulfite sequencing data.  Now we are happy to announce release of the MethylKit BaseSpace Labs app (, which is focused on differential methylation analysis on two groups of bisulfite sequencing samples.  This BaseSpace Labs app is based on the MethylKit R package, published in 2012 in Genome Biology (  The MethylKit app includes these features:

  • Coverage Stats Plot for each sample
  • Methylation Stats Plot for each sample
  • Methylation Correlation Plot
  • Differential Methylation Summary Table (Per Chromosome)
  • Differential Methylation Regions (in csv file and bigwig file)
  • Methylation Stats Summary
  • Methylation Stats Percentile Information

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BaseSpace Dashboard gets a makeover!

We are excited to announce a major refresh for the look and feel of the BaseSpace Dashboard. Based on feedback received on our original dashboard, we created a new dashboard experience that is more intuitive, efficient, and useful. The new Dashboard will be launched as part of our next BaseSpace version release.

We have a video discussing these new features, and the changes are highlighted here as well.

A quick visual comparison of the old vs new Dashboard.

BS Old Look

Old Dashboard


New Dashboard

Some of the important new features and changes include:

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