BaseSpace – Open for Business!

We’re happy to announce the commercial availability of BaseSpace, Illumina’s genomics cloud computing and storage platform.  The commercial release represents a major software update and includes a fully supported BaseSpace Apps store for quick and easy access to Illumina and third-party bioinformatics applications.  As introduced in our previous blog post, BaseSpace e-commerce transactions are based on BaseSpace iCredits, a currency that can be purchased and spent within BaseSpace.

This release also moves BaseSpace out of beta status and includes many new features for both MiSeq and HiSeq users.  Here’s a preview of the new features you will see in the commercial release of BaseSpace:

New BaseSpace Apps Store

The first feature is the BaseSpace Apps store, which is now updated to use iCredits for apps.  Starting today, some apps will charge iCredits, and some apps will remain free apps in the store.

Running your data through a new set of software tools is often difficult. Even if the software package is widely used, the processes of installation, data formatting, and simply evaluating the software tools can be overwhelming.  Clicking on an app within the BaseSpace Apps store brings up a dedicated page with a description, screenshots, and coming soon for some apps, video overviews.  Launching an app is also easy from the Apps store – simply select an app and click on the green button labeled “Launch” to try it out on your own data or on publicly available data in BaseSpace.   We made the Apps store intuitive and easy to use so you can find the right apps for your sequence analysis!


New BaseSpace Apps

BaseSpace continues to attract a large number of app developers who can rapidly make their bioinformatics tools available to enable genomics research in diverse markets including cancer, microbiology, and genetic disease. We’ve added three new apps to BaseSpace with this release, adding to the existing MiSeq Reporter workflows and the new Isaac alignment and variant calling app.  Be sure to check back soon for future blog posts detailing the functionality of these new apps.  Here’s a preview:

HALThe first is a HLA typing application from Omixon Biocomputing (“HLA Typing”).  From Omixon’s app description: The Omixon app performs state of the art HLA typing with accuracy exceeding that of Sanger based typing and is able to do typing based on targeted data, whole exome or whole genome data.  It works with all known HLA alleles, supports 4, 6 or 8 digit typing, and the resolution depends only on the availability of reference and sequencing data.  Additionally, the app is exceptionally fast and easy to use – typing is done within minutes for targeted data, and in 1-2 hours for whole genome data, and the app requires no configuration.

GDAnother new application is from Elsevier Publishing, the world’s leading publisher of scientific and health information.  In a world-first, Elsevier has released a BaseSpace App that enables users submit data directly into the peer-review publication process.

From Elsevier: The Elsevier BaseSpace App works with Elsevier’s new journal Genomics Data, which provides genome-centric reporting on the increasing volume of genomic and functional genomic data that is without a formal report in the scientific, technical or medical (STM) literature. The goal is for authors to provide concise and highly standardized reports summarizing results of microarray or sequencing studies, such as what is put into the BaseSpace cloud. The genomic and functional genomic data/results are intended to serve as points of record that are enriched with interpretative commentary, validated by peer review and verified by a standards-focused editorial team.

PicardSpace_100Finally, we are introducing a new Illumina BaseSpace App called PicardSpace, which calculates alignment QC metrics from a BAM file. The app runs the open-source tool Picard, which was developed at the Broad Institute.

PicardSpace is also a great example for developers of a fully functional web app for BaseSpace. The source code is available in github and anyone can launch the app from the Apps store.

BaseSpace Public Data area

Essential to BaseSpace Apps is the ability to try apps on publicly-available shared data in BaseSpace.  Because of this, we’re introducing the Public Data tab in BaseSpace, which enables you to search and filter datasets by research area and by analytical category.  The screenshot below includes the new filtering interface which will soon be used for filtering apps in the BaseSpace Apps store as well.  Now it’s easy to locate example datasets and match them to the right apps to explore a new analytical workflows or approach.  With BaseSpace’s Public Data area, evaluation of new bioinformatics tools and approaches just became a lot easier!


Sample Sheet Editing and Run Re-Queing

One of the most requested features has been the ability to fix sample sheets and re-submit sequencing runs for data analysis in BaseSpace.  Included in this release is a live sample sheet editor that allows errors to be corrected and for the final sample sheet to be validated – all within BaseSpace.  Once validation occurs, the data, along with the final sample sheet, is automatically queued for analysis.


BaseSpace Download Tool

While we believe that the BaseSpace Apps ecosystem represents a new way to avoid moving, handling, or downloading large sequencing datasets, we recognize that sometimes you just need local access to your data.  While BaseSpace has always allowed you to download your runs or project data, doing so meant relying on your browser’s built-in functionality.  We are now releasing the BaseSpace Downloader which can handle multiple files simulataneously and resume downloads after a severed internet connection.  The BaseSpace Downloader is available for Windows users, and we will continue to expand the downloader to other platforms in the future.


New BaseSpace Web resources

The BaseSpace web pages have received a major overhaul, making it easier to find the information you need about BaseSpace.  This includes major updates to the Illumina BaseSpace home pages (, the BaseSpace login page ( and the BaseSpace developer portal (  On these pages you’ll find links to documentation, technical notes, tutorials and videos.  And we’re not done!  The BaseSpace web pages will be your go-to site for future information, screencasts, and use cases on BaseSpace.

Exciting new additions coming to the webpages are new BaseSpace videos and screencasts.  Ranging from overviews of BaseSpace to focused tutorials, the videos will comprise a set of “push-button bioinformatics” tutorials intended to help get you up and running in BaseSpace.  You can find more information on the BaseSpace home pages as well as on the website such as within the cancer genomics tumor sequencing pages.


Finally, we’ve put together a set of BaseSpace data sheets, technical notes on data transfer and data security, and a comprehensive, authoritative user guide.  Available on the BaseSpace home page and through the BaseSpace help button, the user guide includes information to get started in BaseSpace, interact with your sequencing data and launch apps.


What’s Next

As you can see, the commercial launch of BaseSpace includes a large number of platform enhancements, and this is only the beginning.  As we move forward, we’ll be detailing each new feature in subsequent blog posts.  We’ll also be introducing new BaseSpace Apps as they come onboard.  Stay tuned!

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