Security Update Concerning OpenSSL Heartbleed

We take the security of your data very seriously at Illumina.  As one of many safeguarding measures, BaseSpace uses encryption software to ensure the privacy and security of both your user login information and your sequencing data as it travels from Illumina’s sequencing instruments into our cloud environment.

Recently, a security threat with a common encryption library that is widely used by many websites (including BaseSpace) was found to have a major vulnerability in it.  The security threat was published on April 7th, 2014 for the “OpenSSL” library (CVE-2014-0160 ) and quickly came to our attention.  The vulnerability, nicknamed “Heartbleed”, had the potential to allow an attacker to steal private keys or other sensitive information that is normally encrypted via SSL.  The nickname came about because of the way an attacker could gain access to a server’s memory through the “OpenSSL” specific heartbeat protocol.

Once we assessed the situation we quickly worked with our platform vendor and internal teams to ensure the following was completed:

  • All affected servers were patched with the updated/non-affected version of OpenSSL.  This was completed less than 24 hours after the announcement.
  • All of our public facing SSL certificates were replaced.  All of the old SSL certificates are now being revoked.
  • All login sessions older than 24 hours were automatically invalidated.

We have no information that knowledge of this vulnerability was used against BaseSpace or its users.  However, as with all websites that have updated their OpenSSL libraries, we encourage everyone to change their BaseSpace password.  You should also check your notification history for any suspicious activity.

At BaseSpace, protecting your data is our top priority, and we continue to assess the risks in response to this issue.  We have and will continue to work together with our infrastructure provider, Amazon Web Services, to ensure that all of our services respond quickly to security threats.

For further information about BaseSpace data security, please see our Data Security Technical Note.  If you have any questions or concerns, please feel free to contact support.

Technical Support
Monday – Friday
7:00am – 5:00pm (PT)
858.202.4766 (Fax)

Register Now for the BaseSpace Developers Meeting at EMBL in Heidelberg, Germany


Registration is now open for the BaseSpace Developer’s Meeting at the European Molecular Biology Laboratory (EMBL) Heidelberg, Germany on May 7, 2014.  This free, one-day forum is a great opportunity for both experienced and novice developers to network, exchange ideas, and learn more about the world’s most widely used cloud-based bioinformatics platform for next-generation sequencing.  Participants will use the BaseSpace Native App Engine to launch their own bioinformatics apps in BaseSpace.

Why develop for BaseSpace? Because 90% of the world’s next-gen sequencing data is produced on Illumina instruments, and your novel algorithms, open-source tools, and applications for BaseSpace users can directly impact the growth of genomic research. In short, you can change the way the world analyzes genomic data.


Welcome to EMBL & Illumina’s Co-Hosting of 2014 BaseSpace WWDC
Jonathon Blake, Ph.D., Bioinformatics, EMBL
Raymond Tecotzky, Market Manager, BaseSpace, Illumina, Inc.

Keynote: BaseSpace and The Next Frontier for Genomics Storage, Sharing, and Analysis
Elliott Margulies, Ph.D., Product Owner, BaseSpace, Illumina, Inc.

Biomax PEDANT – Pathway Analysis for NGS Data
Dimitrij Frishman, Ph.D., Professor of Bioinformatics, Technical University in Munich, Germany

New Frontiers of Genome Assembly with SPAdes 3.0 on Illumina BaseSpace Platform
Anton Korobeynikov, Ph.D., Associate Professor Saint Petersberg State University, St. Petersburg, Russian Federation

ABL (Advanced Biology Laboratories/Therapy Edge) DeepChek® Hep B & C Detection App
Dr. Chalom Sayada, CEO, Advanced Biological Laboratories SA

Hands-On Session: Build Your Own BaseSpace App
Greg Roberts, Senior Staff Software Engineer, Illumina, Inc.
Mayank Tyagi, Senior Applications Support Engineer, Illumina, Inc.

Hands-On “Hackathon” Build Your Own BaseSpace App (Choose from Open-Source, Command-Line, or Bring Your Own Code)
Ilya Chorny, Sequencing Application Marketing, Illumina, Inc.

BaseSpace Onsite Introduction – Storage, Sharing, & Analysis in a Box
John Duddy, Senior Staff Software Engineer. Illumina, Inc.

Will be followed by a Networking Reception

Link to Agenda

Event Details:

Date: Wednesday 7 May, 2014 9:00-6:30 PM

EMBL Heidelberg
Meyerhofstrasse 1
69117 Heidelberg, Germany
Flex Lab A+B

Cost: Free

Twitter: #basedev2014

Got a killer NGS app? Enter your original idea and win an iPad mini at the conference!

Register Here

Downloading Your Data Just Got A Lot Easier

In the past year, we’ve seen the usage of BaseSpace along with the number of apps continue to increase.  There are times, however, where you just need local access to your data.    Today, the BaseSpace team is happy to announce one of our most requested features; an easier, faster download application. 

The new BaseSpace downloader is a one-time install desktop application on Windows Vista, 7, 8 and 8.1 and on Mac OSX 10.7 +.  It has been specifically built to handle large file downloads in a reliable and efficient manner.


New Download Options

There are now several ways to download data from BaseSpace.  

  1. Download an entire project
  2. Download one or more analyses
  3. Download one or more samples
  4. Download one or more individual files

The first way is to download the whole project.  When on the project page, click the “Download Project” button as seen below.


Your next option is to download an individual analysis or multiple analyses.  By checking the analysis, the download button will show “Download Analyses”.


Another option you have is to download individual samples.  Looking at the samples list in the project, you can similarly check one or more of those samples and the button will show “Download Samples”.


After clicking on the download button we ask for confirmation.  If you have never installed the app then click on “Install the Downloader”. 

BaseSpace Downloader -3



We are excited about this feature and look forward to your feedback!



Nextera Rapid Capture Exome: New data sets, new manifest, and new analysis tools!

We are happy to introduce two new Nextera Rapid Capture Exome data sets in BaseSpace:

  • 12 exome samples sequenced (on 1 flow cell) on HiSeq 2500®
  • 1 exome sample sequenced on MiSeq

These exome data sets demonstrate the accuracy of the HiSeq 2500 & MiSeq sequencing platforms, the improved enrichment metrics from using the new targeted region manifest v1.2, and the power and ease of use of the BaseSpace BWA Enrichment App.

Be sure to take a look and compare the difference between the data sets analyzed with manifest v1.1 and v1.2. Both manifest versions are available for use in BaseSpace now.  The v1.2 manifest files will be available for download from the Illumina support web site in the near future and a URL will be provided in an update to this blog post.

Click on the links below to see the project and run folders. You will be asked to “Accept” the Run/Project into your BaseSpace account: this is the same mechanism you would use to share BaseSpace projects or runs with your colleagues/collaborators via a dedicated URL.

  • HiSeq 2500: Nextera Rapid Capture Exome (12plex, CEPH Trio replicates): Project (Sample data & analysis results), Run (QC plots & run summaries).
  • MiSeq v3: Nextera Rapid Capture Exome (NA12878): Project (Sample data & analysis results), Run (QC plots & run summaries).

Materials and Methods: Human Coriell CEPH trio samples NA12878, NA12891, and NA12892; Nextera Rapid Capture Exome kit; analysis with BaseSpace BWA Enrichment App.

Learn more about exome sequencingNextera Rapid Capture Exome Kits, and BaseSpace Core Apps.

BaseSpace Update from AGBT

We are humbled and excited by the overwhelming attention BaseSpace, BaseSpace Onsite, and the BaseSpace Core Apps have received at AGBT. Things were set in motion on Wednesday by a review of the BaseSpace RNA-Seq Apps (TopHat and Cufflinks) by James Hadfield from Cancer Research UK as a part of his presentation at the Illumina User Meeting. Then on Thursday, during the standing-room only Illumina Workshop, our own Gary Schroth gave a “User’s Perspective” talk on RNA-Seq right after Sheila Fisher’s hot-off-the press presentation of HiSeq X10 and NextSeq datasets from the Broad Institute. Gary gave a deep dive of the TopHat and Cufflinks Apps on BaseSpace. Gary emphasized the high usability and the end-to-end workflow now enabled by BaseSpace. The workflow starts with creation of samples, libraries and runs for the NextSeq on the Prep tab, followed by real-time monitoring of sequencing metrics, and finally the streamlined analysis of data resulting in graphical interactive plots of expression profiles. Gary also mentioned that he is not a bioinformatician, but can now perform RNASeq analysis all by himself.

On Thursday evening, the first-ever AGBT “Electronic Poster Session” was held, where about 30 software vendors showcased their solutions in a large, well-catered room (chocolate fountain, crabs, sushi and all). The two of us who were demo-ing BaseSpace were kept busy throughout the two hours and we definitely got the sense that the value proposition of the BaseSpace platform and Apps resonated with all users who stopped by our booth.

Finally, we would like to respond to some questions that have come up in the twitter-verse based on the James Hadfield and Gary Schroth presentations:


1. To cite BaseSpace in journal manuscripts: we recommend citing the specific URL as appropriate

  • To cite BaseSpace in general:
  • To cite a particular App:  etc. (Each App has a dedicated “App description page” that is accessible from the App tab on the top menu bar)
  • To cite algorithms/methods used in the Apps:  All the methods used within apps are referenced within the corresponding App description page
  • To cite a particular Project, with embedded datasets and App analysis sessions, again use the particular URL associated with the dataset. Here is an example of a publicly shared Nextera Rapid Capture Exome project, with 12 exome samples run on the HiSeq 2500 (you will notice the associated “Analyses” and “Samples” along the tab on the left) :

2. Timing of availability of the BaseSpace Core Apps: The BWA/GATK whole-genome (WGS) App, the BWA/GATK Exome (Enrichment) App, as well as the Strelka-based Tumor-Normal App are available on BaseSpace today.  The Isaac-based WGS and exome Apps, along with the RNA-Seq Apps will be available by the end of February.

BaseSpace Updates: NextSeq 500 and More

It’s barely midway through the first month of 2014, and we already have breaking news to share. First and foremost, we are excited to announce that the NextSeq 500 Sequencing System integrates seamlessly with BaseSpace. In fact, we have made a number of significant improvements to the BaseSpace platform in support of this new instrument, such as sample and run management with our new Prep Tab feature (more details below).  Last but certainly not least, we’ve also introduced a number of new BaseSpace Apps that we call “Core” Apps for all of Illumina’s sequencers, adding to our increasing range of core competency for data processing for the most popular sequencing applications.

Seamless Integration with NextSeq 500


Much like the MiSeq, the NextSeq 500 System features a load-and-go workflow, where users simply load the flow cell and reagent cartridge onto the instrument. The NextSeq Control Software interacts directly with BaseSpace to retrieve run information entered in the cloud, performs a series of checks, and starts the sequencing run. Base calls and performance metrics generated on the instrument are instantly transferred to BaseSpace (or the new BaseSpace Onsite System, more on this below), saved to an independent local server, or both. Users can review real-time performance metrics on the instrument or by logging into BaseSpace from any web browser.

Prep Tab for NextSeq


One of the most useful new features in BaseSpace is called the Prep Tab. Using the Prep Tab, you can plan your entire workflow from sample creation, to library prep and pooling, to sequencing.  Within the Prep Tab, researchers can plan sequencing runs in four easy steps, tracking thousands of samples and experiments without complicated spreadsheets. The intuitive interface prompts users to enter or import sample information, place samples onto library preparation plates, and pool libraries for sequencing. Syntax errors are checked at each step of the process.  Before sequencing runs begin, index compatibility is automatically confirmed. Once a run has been planned and is ready to sequence, you simply select the run. There is no additional setup required on the instrument and no sample sheets – it’s all integrated in BaseSpace!


While this functionality is currently only available on NextSeq instruments, it will soon be updated to function for HiSeq and MiSeq instruments. For now, HiSeq and MiSeq instruments will continue to use Illumina Sample Sheets.

Introducing BaseSpace “Core Apps”


BaseSpace “Core Apps” include four of the most common NGS secondary analysis workflows: whole-genome sequencing, exome sequencing, tumor/normal whole-genome sequence analysis, and transcript assembly and expression profiling.  Due to the unique scalability of the cloud, the number of samples, or the amount of data per sample can be scaled up to meet even the most demanding research needs.  The first Core Apps to appear in BaseSpace today (adding to the existing Isaac App in BaseSpace) are the popular BWA+GATK Apps for whole-genome and enrichment sequencing and tumor/normal whole-genome analysis.  We will shortly be adding apps that include Illumina’s own fast and accurate Isaac aligners and variant callers as well as industry workhorses Tophat and Cufflinks for alignment and differential expression profiling and detection of gene fusions.  And all of this is in addition to the existing MiSeq Apps in BaseSpace!

Core App Key Feature Advantage
RNA-Seq_Align_100Tophat Alignment RNA-Seq alignment using industry-standard tool, seamlessly integrated into the Cufflinks Assembly & Differential Expression App Works with all samples, either fresh-frozen or FFPE
RNA-Seq_DiffEx_100Cufflinks Assembly and Differential Expression Differential expression and gene fusion calling, with pre-formatted, interactive reports allow aggregation of multiple samples Quickly assess expression levels and drill down on significantly expressed genes/ isoforms
WholeGenomeSeq_100WGS Choose BWA Alignment and GATK Variant Calling, or Isaac Alignment and Variant Calling  to detect SNPs, indels, copy number variations, and structural variations Interrogate a wide variety of samples using a unified analysis method
Exome_100Exome Enrichment* Choose BWA Alignment and GATK Variant Calling for exomes, or Isaac Alignment and Variant Calling for exomes Zero in on sample results and variants with a single click; quickly identify off-target rates and biological context of SNVs and indels across all your samples
Tumor_Normal_100Tumor/Normal Analysis Combined analysis of whole-genome tumor/normal data to detect SNPs, indels, copy number variations, and structural variations Comprehensive assessment of the largest number of somatic events

*For data generated with Nextera Rapid Capture Kits

BaseSpace Onsite System


We’re also very excited to introduce the BaseSpace Onsite System, a local version of the BaseSpace cloud that enables researchers to keep all NextSeq 500 System data on site. Designed for installations that cannot connect to the internet, BaseSpace Onsite offers many of the features and benefits provided by BaseSpace Cloud such as real-time data transfer and industry-standard security.  Its intuitive interface guides users through sequencing experiments, from run preparation and sample management to variant calling. BaseSpace Onsite is easy to install, maintain, and scale, bringing simplified data management, analytical sequencing informatics tools, and storage directly to researchers, while minimizing the need for bioinformatics and IT assistance.

Stay tuned for more BaseSpace improvements in the coming year.

Wishing you Happy Holidays with a Festive Competition!

As we near the end of the year, we’d like to share a fun competition put together by James Hadfield, director of the genomics core facility at the University of Cambridge, Cancer Research UK Cambridge Institute, and sponsored by Illumina and BaseSpace.  James is a blogger at CoreGenomics, and is running a holiday contest that will test your knowledge of library prep and sequencing applications. How much do you know about the cost of library prep and sequencing for various applications, including genome sequencing, RNA-Seq, Exome Seq and others? Take the CoreGenomics logic challenge and find out!

The winner of this festive competition will receive a MiSeq 600 cycle run to be performed in James’ lab, and 250 iCredits towards BaseSpace analysis. You’re in charge of library prep, and of course, the sample for sequencing, although James may lean towards seasonally appropriate species such as the cranberry or fir tree genome, (our pick: follow up study on the Reindeer rumen microbiome).

So check out the CoreGenomics post here, with a link to enter the contest, as well as all the rules and regs. We’re happy to help support this fun exercise by covering the kit and the iCredits.

Happy Holidays from Illumina and the BaseSpace team!