Archive by Author | Jay Patel

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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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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BaseSpace Support for MiniSeq

The latest addition to the Illumina sequencing platform portfolio, MiniSeq, is integrated with BaseSpace.

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Align Custom Genomes, Improve Scaffolding for de novo Assemblies, and more with our latest BaseSpace Labs Apps

The BaseSpace Labs team have kept busy in recent months, bringing multiple new apps and improved functionality for existing apps to BaseSpace. Our new and improved tools enable alignment of custom genomes with BWA, improved scaffolding for de novo assemblies, coordinate mapping conversion from one human assembly to another, and more!

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New and Updated Illumina Core Apps

Since our last app news in August and September, we’ve published more than 15 new and updated apps in BaseSpace! Let’s explore five of those:


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