Enhancements to Run Monitoring

We’ve recently added some improvements to the Sequencing Runs list. These updates should help to quickly get basic quality information about each run, without needing to click into Run details pages.

For example, % reads passed filter (%PF), average %Q30, yield, and cycles (for Read1 and Read2) are now columns on the Runs list.

Run Quality Metrics

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New RNA-Seq Alignment App with support for TruSight RNA Pan-Cancer and more

With the launch of the TruSight RNA Pan-Cancer panel, a targeted enrichment panel for the detection of variants, fusions, and gene expression profiles in 1385 cancer-associated genes, Illumina is pleased to provide an intuitive BaseSpace App, RNA-Seq Alignment v 1.0, that supports simple push button analysis of the data.

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RNA-Seq Alignment

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Announcing File Upload with BaseMount

We are pleased to announce a new release of BaseMount, our FUSE driver to mount your BaseSpace account as a Linux filesystem.

BaseMount allows you to navigate on the command line 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 allows you to download – and now upload – files, but maybe more importantly, it allows you to work interactively with your files stored on BaseSpace without having to download them. You may, for example, run samtools directly on a large BAM file, and it will only fetch the blocks needed for your query.

This update (BaseMount v0.12) includes:

  • Write-mode: project and appresult creation, file upload
  • Properties can be viewed and edited
  • Improved documentation
  • Relaxed timeout for low bandwidth
  • Unmount assistance, listing blocking processes and offering lazy-unmount

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Human mtDNA Analysis in BaseSpace

Mitochondrial DNA (mtDNA) analysis enables forensic laboratories to extract genetic data from small biological samples, found in less than ideal condition. Mitochondria in humans cell contain about 1,000 copies of mtDNA. The ease-of-use of next-generation sequencing (NGS) and Nextera XT enables labs to speed up their workflow, reducing time and labor spent on prep, and generate deeper coverage data compared to Sanger sequencing at 1X coverage/rx.

The updated Illumina mtDNA demonstrated protocols provide a complete mitochondrial DNA solution – from targeted library prep and sequencing to bioinformatics analysis and report generation in BaseSpace – to help investigators draw conclusions in a straightforward and intuitive workflow.

The two new mtDNA apps in BaseSpace allow for variant analysis and easy visualization of mitochondrial sequence data. This workflow can analyze any part of the full circular genome, without any origin dead zone, using quality and coverage thresholds customized by the user (Figure 1).

Figure 1: mtDNA Analysis Workflow. Sequence data is streamed into BaseSpace. Initial processing is performed using the mtDNA Variant Processor app and the results are stored in your BaseSpace project. Use mtDNA Variant Analyzer to visualize the data and generate a downloadable Excel report.

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Introducing BaseSpace Professional!

The BaseSpace team is excited to introduce the BaseSpace Professional tier, which enables access to a host of new features and services, including:

  • Multi-user access with Workgroups
  • 8 hours of Bioinformatics Professional Services from Illumina
  • Expandable storage and compute credits

With BaseSpace Professional we are releasing a new Workgroup feature to enable seamless and efficient data sharing for you and your colleagues. Workgroups enable collaboration on a global scale.

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Introducing BaseSpaceCLI

In July, we released an early-access version of BaseMount, a command-line tool to allow you to navigate your BaseSpace account and work with your files on-demand.

To complement this browsing capability, we are adding to the suite of BaseSpace Command Line Tools by releasing the BaseSpaceCLI (Command Line Interface). BaseSpaceCLI provides two new areas of functionality, uploading samples and launching apps, but also comes with a host of other commands to help you work with your BaseSpace data and apps.

BaseSpace Command Line Tools

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Meet the New BaseSpace

We’ve updated BaseSpace to give it a sleeker, more modern look and to simplify the interface, all without compromising the core functions that you’ve come to rely on.

Our BaseSpace design and development teams focused on making it easier for you to access relevant information and tasks, and harmonized the new design with the visual attributes you see in our instruments, like luminosity, transparency, and vibrancy.

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