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Updated Command Line Tools – Wait for App Dependencies

We are pleased to announce a minor release of BaseSpaceCLI (0.8.10) with some improvements to existing tools and a new tool – bs wait.

‘bs wait’

The new wait command for BaseSpaceCLI is analogous to the shell command wait and was designed to help connect together separate app launches. The wait command accepts as arguments one or more appsessions and will then wait for these appsessions to finish, polling based on a specified interval (default 60 seconds). Once they have all finished, bs wait returns the appresults that have been generated by the provided appsessions. The intention is that these appresults can then be passed into another app launch, providing some limited app-chaining capabilities.
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New BaseSpaceCLI Tools

We are pleased to announce the third release (version 0.8) of BaseSpaceCLI, which includes a major new tool and a number of minor features. To install the new release, run this script:

$ sudo bash -c "$(curl -L https://bintray.com/artifact/download/basespace/helper/install.sh)"

BaseSpace Copy

With this release of BaseSpaceCLI we are introducing a new high-performance copy tool called BaseSpace Copy or bscp, which provides the following features:

  • Rich and flexible URI mechanism to specify source and target for copies
  • Multi-threaded for performance and to cope with high-latency connections
  • Excellent data integrity, all part data is hashed and verified. Ability to export md5sum compatible sum file for future data verification.
  • Resumable downloading

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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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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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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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Monitor your Sequencing Runs and Analyses from your iOS Device!

basespace-mobile-iconIntroducing the BaseSpace mobile app!

We are very excited to announce the availability of the new BaseSpace iOS mobile app. With this app you can now monitor your BaseSpace runs and analyses more easily than ever before using any compatible mobile iOS device running iOS 8.4 or newer! This includes the iPhone 4S and later, and iPad 2 and later devices.

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