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Welcome to the new BaseSpace® Sequence Hub!

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Next-generation sequencing (NGS) systems now produce more data than ever before. Additionally, a typical NGS workflow involves manual, time-consuming touchpoints for quality control, analysis setup, and results review. As a result, labs who perform NGS or other complex, high-volume processing of samples can be overwhelmed managing the workflows and data generated. To address these issues and simplify NGS research, we are happy to announce the new version of BaseSpace Sequence Hub. It is designed to enhance your laboratory’s efficiency and support the needs of high-throughput labs.

Included in this update are new features, including a biosample-centric data model that provides tracking of all biosample activity from lab preparation through analysis delivery. We’re also introducing the following features:

  • New automation quality control features
  • Automated app launches and workflows
  • An updated Application Programming Interface (API) to help you streamline your next-generation sequencing (NGS) workflows
  • An improved user interface that helps you access your data and perform functions more quickly

New Features

Biosample-centric Data Model

Our new biosample-centric data model enables easy tracking of all biosample activity from lab preparation through analysis delivery. Biosamples are the data containers that represent the original DNA source material. They are used to trace all sequencing activities, including lab preparation (with LIMS integration) sequencing runs, data analysis, and delivery of data.

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Figure 1 Access all libraries, runs, requeues, analyses, and datasets associated with biosamples from a single place.

The new data model centers on biosamples, the original source of DNA, so you can easily track all biosample activity from lab preparation, with optional laboratory information management system (LIMS) integration, to delivery of analysis results. Biosamples can be used as inputs to multiple sequencing runs, and they can contain multiple datasets, which can live within separate projects.

Important Note: Biosamples with the same name (Sample ID in the sample sheet) are automatically aggregated. The new features will aggregate all FASTQ data sets with the same Sample ID into a single biosample. It is important to name the samples in your sample sheet uniquely, otherwise they will be aggregated together. Learn more about automatic data aggregation here.

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Figure 2 Samples have been replaced by biosamples as inputs to apps.

Automated Lane QC, App Launch, and Analysis QC

After sequencing, much of the work required to process biosamples can be automated in bulk. By setting up automation ahead of time using the command line interface (CLI), sequencing runs can be automatically passed or failed based on their sequencing quality, converted to FASTQ datasets, used as inputs in an app, and then be passed or failed based on their app metrics. Automation removes much of the time-consuming and error prone manual work of processing sequencing data into downstream results.

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Figure 3 View lane metric details to understand why a lane may have failed.

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Figure 4 A comparison of the number of touchpoints when using the new automation features of BaseSpace Sequence Hub

Improved User Interface

The updated interface provides quick access to all of your data from the My Data menu, while the new Action Toolbar contains new and improved app functions such as requeues, QC status changes, workflows, and collaboration tools.

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Figure 5 The new Action toolbar contains app functions like requeues, QC status changes, workflows, and collaboration tools.

The Analyses page provides a listing of all analyses in your account. The filters on this page help you quickly narrow your search for specific analyses by their current status.

The Projects and Runs pages function the same as before, providing quick access to all of your sequencing projects and instrument runs.

Advanced Automation and Integration Toolset

Alongside our updated data model, we’ve introduced version 2 of the API, which enables you to interact directly with your data and integrate systems together with your BaseSpace Sequence Hub account.

The new automation tools in version 2 of the API:

  • Correspond to the new biosample-centric data model
  • Improve performance and robustness of the solution
  • Include new documentation

Note: The version 1 API is still fully-supported and maintained, although we are actively focusing primarily on version 2 API development. The version 1 API documentation is maintained here.

Version 2 of BaseSpaceCLI has been built using the version 2 API. BaseSpace CLI can be leveraged to read data from your BaseSpace Sequence Hub account and create new data by uploading data and launching apps. In addition, the new BaseSpace CLI can be used to create automated analysis workflows, and import biosamples.

BaseMount is a command-line tool which allows you to explore through runs, projects, biosamples, and datasets, and interact directly with the associated files exactly as you would with any other file system.

We hope the new functionality of BaseSpace Sequence Hub enables your lab to boost productivity and discovery. Visit our updated Support Site to learn more about how to use all the new features and tools. Please contact us at techsupport@illumina.com if you have any questions or comments.

Sincerely,
The BaseSpace Sequence Hub Team

References

  1. CLI documentation https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview
  2. CLI automated workflow creation docs https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-examples
  3. Link to v1 API docs https://developer.basespace.illumina.com/docs/content/documentation/rest-api/v1-api-reference
  4. Link to v2 API docs https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference

 

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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