Archive by Author | Michael Janis

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

BSEMBLB

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.

Agenda:

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

Location:
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

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

NextSeq500

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

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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!

plateOnly2

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”

BaseSpaceApps

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

onsite

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!

Whole-genome and cancer analysis: Datasets from Illumina’s FastTrack Services Laboratory

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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.

See you at #basedev2013 in San Francisco

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.

Register here, or join us Monday from 8:00 AM–6:00 PM at the JW Marriott San Francisco Union Square, Metropolitan room.

If you can’t join us in person, follow #basedev2013 from @illumina for highlights.

MiSeq Trio Data: TruSight One Sequencing Panel

We’re happy to introduce a dataset from the TruSight One Sequencing Panel, which provides comprehensive coverage of 4,813 genes with an associated clinical phenotype. With TruSight One, you can analyze all of the genes included in the panel, or focus on a specific subset of them. Labs can use this panel to expand existing assay offerings, streamline workflows, or create an entire portfolio of sequencing options.

This is a shared, downloadable dataset in BaseSpace representing a family trio using TruSightOne sequenced on a MiSeq using v3 reagents. This trio was obtained from the Coriell Institute’s NIGMS Human Genetic Cell Repository, and is from the CEPH/Utah Pedigree 1463.

Sample ID Sample Name Details
1 NA12880 Daughter
2 NA12878* Mother
3 NA12877 Father

* From the Coriell Institute“Donor subject has a single bp (G-to-A) transition at nucleotide 681 in exon 5 of the CYP2C19 gene (CYP2C19*2) which creates an aberrant splice site. The change altered the reading frame of the mRNA starting with amino acid 215 and produced a premature stop codon 20 amino acids downstream, resulting in a truncated, nonfunctional protein. Because of the aberrant splice site, a 40-bp deletion occurred at the beginning of exon 5 (from bp 643 to bp 682), resulting in deletion of amino acids 215 to 227. The truncated protein had 234 amino acids and would be catalytically inactive because it lacked the heme-binding region.”

This data, along with other example datasets from a variety of sequencing runs, is available for import into your BaseSpace account from BaseSpace’s Public Data repository:

dataCentral

To access the data, click on the links (the full URLs are shown below) to view the Project (enrichment results) or the Run (sequencing results).  You will be asked to “Accept” the Project or Run into your BaseSpace account.  Once there, you can access or download the data.

Some stats for this dataset:

Library Prep Kit TruSight One Sequencing Panel
Sequencing Kits MiSeq Reagent Kit, v3
Sequencer MiSeq
Read Length 2 x 151 bp
Sample Multiplexing 3 samples
Sequencing Output 9.4 Gb
Cluster Density 1325 +/- 27 K/mm2
Cluster PF 92.25  +/- 0.74%
Reads PF 29.84 M
Total Aligned Reads 15,589,287 – 20,773,100
Read Enrichment 63.4% – 66.1%
Uniformity of Coverage (% > 0.2 of mean) 95.5% – 96.4%

Run data link: https://basespace.illumina.com/s/7am28MijIfVt

Project data link: https://basespace.illumina.com/s/zSlj15ZMV4EA

Register Now for the BaseSpace Developers Meeting in San Francisco

BSdevConf1

Registration is now open for the BaseSpace Developer’s Meeting in San Francisco, CA on December 9, 2013.  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.  As with the first Developer’s Meeting in Bostonparticipants will use the new 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.

Agenda:

Keynote: BaseSpace: Leveraging the Cloud to Eliminate the Bioinformatics Bottleneck
Alex Dickinson, Senior Vice President, Cloud Genomics, Illumina, Inc.

The BaseSpace Ecosystem: A Growing Opportunity for End Users and Developers
Scott Kahn, Chief Information Officer, Illumina, Inc.

BaseSpace Apps — Is One Enough?
D. Matthew Landry, CEO DxEngine/CTO, Biomatters Ltd.

New BaseSpace App Developer Experience
Zayed Albertyn, P.h.D., Co-Founder and Bioinformatics Director, NovoCraft Technologies

Rapid App Development with BaseSpace: Hello World! App — Developed in Two Days
Scott Markel, Ph.D., Principal Bioinformatics Architect, Accelrys

Developer to Developer — How the BaseSpace Architecture Makes it Easy to Develop and Launch Apps
Greg Roberts, Development Leader, BaseSpace, Illumina, Inc.

Hands-on Workshop – How to Build an App for That

Will be followed by a Networking Reception

Link to Agenda

Event Details:

Date: Monday 9 December, 2013, 8:00-6:00 PM PT

Location: JW Marriott San Francisco Union Square
515 Mason Street
San Francisco, CA
Metropolitan Room

Cost: Free

Twitter: #basedev2013

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

Register Here