Archive by Author | PrithwishPal

New FASTQ Generation App on BaseSpace

As part of the latest release of BaseSpace, we are pleased to announce an update to the FASTQ generation process that will provide a faster, richer experience for HiSeq and NextSeq users.


Our new FASTQ Generation tool provides two new major benefits:

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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.

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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BaseMount: A Linux command line interface for BaseSpace

BaseSpace was designed with a graphical, web-based interface to enable push-button analytics, and sharing of NGS data. We also realize that there are some use cases, especially while working with bulk data, where a Linux-based command line interface (CLI) is more convenient.  We are therefore happy to announce the early access release of BaseMount, a tool that can be used to mount your BaseSpace data as a Linux file system. With BaseMount you can navigate 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 is a FUSE driver, which operates in user-space and uses the BaseSpace API to generate the file system structure for both the metadata and actual file-based data.

To install, please go to the BaseMount page: and run the installation script. We have several tutorial videos as well as a Help Page to get you started. The Help page also has information on hardware and operation system requirements.

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Overhaul of SAV Charts

As part of the latest release of BaseSpace, we have made some changes to the Run charts by adding interactive functionalities such as zoom, pan, and scale for certain charts.

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Illumina Informatics at Bio-IT World 2015

We are excited to be part of the Bio-IT World Conference & Expo 2015 starting today at the Seaport World Trade Center in Boston, MA.  Representatives from the BaseSpace and NextBio teams will be at the conference, and are looking forward to engage with Bio-IT attendees. Stop by our booth #129, or connect through Twitter (@BaseSpace) to discuss our portfolio of cloud and on-site genomic storage, analysis and interpretation solutions: BaseSpace cloud, BaseSpace On-site, NextBio Research, & NextBio Clinical.

We will have an in-booth demo of the NextBio Clinical platform at 10.05am (as part of the ‘Best of Show’ program).

Plus, join us for our lunchtime presentations on Wednesday, April 22.

  • Track 5 (12:40pm):  “Sample Aggregation and Analytics in the Post-$1,000 Genome Era” 12:40 PM presented by John Shon, VP, Bioinformatics & Data Sciences
  • Track 9 (1:10 PM): “Enterprise Informatics: A High-Performance Application Development Platform for Collaborative Genomics Research” presented by Paul Flook, Ph.D., Sr. Director, Enterprise Informatics

And stay an extra day in Boston for the BaseSpace developers conference at The Broad Institute. Register here.

See you all in Boston!

Support for Internet Explorer 9

Coinciding with the release of BaseSpace v3.16, we are officially discontinuing support for Internet Explorer 9 (IE9). After April 17, 2015, users will no longer be able to run BaseSpace on IE9.

With the IE browser having undergone two major upgrades (latest version is IE11), we only have a small number of users accessing BaseSpace via IE9. More importantly, with rapid evolution of browser features, the technical burden of supporting old browsers slows down development of newer features.

We apologize for any inconvenience, but encourage you to either upgrade to the latest version of Internet Explorer (IE11), or choose other supporter browsers such as Chrome, Firefox, or Safari.