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.

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