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.
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: basespace.illumina.com
- To cite a particular App: https://basespace.illumina.com/apps/303303/BWA-Enrichment 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) : https://basespace.illumina.com/projects/3289289/
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.
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!
*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.
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!
We are pleased to announce the availability of data from two sequencing projects conducted in the Illumina FastTrack Services Laboratory through the Illumina Genome Network (IGN). Whole-genome and Cancer Analysis Demo Datasets can now be accessed within or downloaded from BaseSpace for free through BaseSpace’s Public Data repository.
Whole-Genome Analysis Dataset:
Results from the ENCODE project reveal that many DNA variants previously associated to disease lie outside of the coding regions of genomic DNA. Because whole-genome sequencing (WGS) gives researchers the most complete view, we offer the Illumina FastTrack Services Whole-genome Demo Dataset containing three WGS example datasets using the CEPH family trio sequenced to depth of ~30x coverage and analyzed using the Whole-Genome Sequencing Informatics Pipeline v2.0. The project includes archival BAM files, variant calls (CNV, SV, & SNPs), a sample PDF summary report, and Illumina Omni2.5M genotyping data.
To access the shared whole-genome dataset in your BaseSpace account, click the following shared project link: https://basespace.illumina.com/s/dOTDV9brOuJJ.
Cancer Analysis Dataset:
Cancer possesses significant heterogeneity at the genetic and histological levels. The Illumina FastTrack Services Cancer Analysis Demo Dataset uses the IGN variant calling and sequencing methodology to address this complexity using ATCC_HCC samples sequenced to 40x coverage for the normal tissue sample and 80x coverage for the tumor tissue sample. The data is analyzed using Cancer Analysis Pipeline v2.0, which uses a Bayesian combined variant calling method that provides the most accurate models for real-life tumor samples, recovering 97% of known SNVs. The datasets include the standard WGS deliverable, as well as somatic variant data, and somatic PDF summary report.
To access the shared cancer analysis dataset in your BaseSpace account, click the following shared project link: https://basespace.illumina.com/s/lAkSmtRTYN1Z.
More About the Illumina Genome Network:
The IGN, consisting of CSPro-certified organizations and Illumina FastTrack Services, offers highly accurate, affordable, end-to-end human whole-genome sequencing services. The IGN laboratories have experienced scientists using TruSeq technology for superior coverage and quality of even challenging regions, and industry-leading HiSeq systems for the highest throughput. IGN Services are finalized with data analysis by skilled bioinformaticians to accelerate researchers’ opportunities to discover more from the whole human genome.
We invite you to view these example IGN projects using BaseSpace Apps such as the Broad’s IGV, or by downloading files and exploring the data using your favorite tools. See for yourself the unmatched performance, data quality and expertise of the Illumina Genome Network.
In the San Francisco Bay area this week? Drop by the BaseSpace Developer Conference on Monday, December 9.
Network, exchange ideas, and learn about making genomic apps for BaseSpace, the world’s most widely used cloud-based bioinformatics platform for next-generation sequencing. Build an app in less than three hours in the afternoon hands-on session.
Novice and experienced developers, researchers, engineers, academic and industry professionals welcome. Learn from the community, and start changing the way the world analyzes genomic data. In one day. For free.
If you can’t join us in person, follow #basedev2013 from @illumina for highlights.
We are excited to announce a brand new look for Projects and Analyses in BaseSpace. We have made significant improvements to the ways in which users interact with their Analysis data. We strive to bring our users the best experience possible and we hope that you enjoy these changes.
Here is a brief summary of all of the changes you will see:
- New look and feel to the Project page: With this new look, you should be able to navigate around your projects more efficiently.
- Streamlined left-hand navigation: Everything you need from your project, whether it’s your input, output, or samples; it’s accessible through this navigation.
- What we used to call AppSessions, we now call Analyses: the output of BaseSpace Apps.
- Improvements to the Analysis page
- Improvements to the file browser
- Visual improvements to the file browser allows for simpler navigation of your results. Select a file, and open it right in BaseSpace.
A Note About Apps and Analyses
A new Analysis is created each time you launch an app. You can find a list of Analyses within each Project. Each time data in a Project is selected as input to run an app, an Analysis is created in that Project. In addition, each time a Project is selected for storing result data, an Analysis will also be created in that Project. On each Analysis page, you will find:
- Information about the app that performed the analysis
- A running status update from the app
- The result files that were uploaded to your account once the app’s analysis was completed
- The input data selected for the app via the Analysis Inputs page
You can also rename each Analysis you own by clicking on the Edit Analysis button on the Analysis page.
This will allow you to more easily organize your results in BaseSpace.
For more information, please refer to the BaseSpace Release Notes. Please do not hesitate to provide feedback to us via the Contact Us button, we constantly strive to improve BaseSpace for our users.