Archive by Author | Swathi Ramani

New Sequence Quality Metrics in BaseSpace™ Sequence Hub

The Run Monitoring features in BaseSpaceTM Sequence Hub (BSSH) enable users to remotely monitor the quality of their sequencing runs and troubleshoot sequencing errors. As part of our efforts to extend real time Run Monitoring capabilities, we recently released new data quality metrics in BSSH.

 

% Occupancy for iSeq™ and MiniSeq™ instruments

 In a previous release, we added the %Occupied measure in the Charts section of Run Monitoring for the NovaSeq™ systems. As part of this release, this metric will now be visible for iSeq and MiniSeq systems, in BaseSpace Sequence Hub. This measure can be used to understand loading concentrations on the flow cell.

For patterned and non-patterned flow cells, % Occupancy is the percentage of clusters on the flowcell that have DNA that can ultimately be sequenced. With patterned flow cells (such as iSeq), the number of nano wells on the patterned grid determines the total number of possible clusters. For non-patterned flow cells (such as MiniSeq), the total number of possible clusters is the number of non-duplicated spots identified by Real Time Analysis (RTA) during template generation.

 

new metrics

 

% Pass Filter (%PF) settings for all instruments

 The Flow Cell chart in BaseSpace Sequence Hub has also been updated to include the %Pass Filter (%PF) for all instruments. This additional information will allow users to determine in particular tiles of a flowcell have unusual levels of %PF.

%PF

With these enhancements, we have added capabilities that are currently not available in Sequence Analysis Viewer (SAV). SAV will be updated in the future so our users have a consistent experience across SAV and BSSH.

 

#QB6200

Putting Your Privacy First

BaseSpace™ Sequence Hub is used by investigators around the world to facilitate and scale their sequencing and genomic data analysis operations. At Illumina, we understand that security, privacy, and confidentiality are complex issues, and we are committed to protecting our software-as-a-service (SaaS) customers’ data.

To ensure that our customers remain compliant with upcoming changes to the EU General Data Protection Regulation (GDPR), we’ve made a number of updates to privacy practices, policies and agreements that are effective May 25, 2015 for all users globally.  These changes include explaining in more detail how we use your information, including your choices, rights, and controls.

Privacy and compliance is a shared responsibility between Illumina and our customers. We are responsible for the security of the BaseSpace Sequence Hub platform. Our cloud provider, Amazon Web Services (AWS) is responsible for providing the tools, services and functionality that enable both the data controller (our customers) and the data processor (Illumina) to be successful.

 AWS-ILMN_Shared_Responsibility_Model

Figure 1: Shared responsibility Model

 

A short summary of our changes:

  • GDPR and Terms & Conditions (T&Cs). GDPR places new obligations on organizations that process EU personal data. As a result, we have updated our business operational practices. The following documents (Privacy Policy (Link), and Terms & Conditions (Link)) better explain our customers’ and users’ rights, and their relationship with Illumina. In addition all our NGS product support pages have been updated with a Privacy & Security section (Link).
  • Improved clarity and transparency.As a key part of GDPR compliance, we’ve described our data processing practices in clear language. For instruments sending Performance Data (IPD) to BaseSpace Sequence Hub, or connected in the Run Monitoring or Storage and Analysis mode, our updated Illumina®Proactive Technical Note (Link) clearly explains what data is sent to BaseSpace in each of the connectivity modes.
  • Data Protection Addendum:BaseSpace Sequence Hub leverages AWS to deliver its services. The updated AWS Service Terms (Link) incorporate the GDPR Data Processing Addendum (DPA) and will automatically apply to all customers. Illumina is willing to sign a DPA for customers who ask for it.
  • Opt-in & Opt-out:Sharing data with BaseSpace Sequence Hub, irrespective of connectivity mode, is entirely controlled by our customers. If you would like to opt out of sharing Instrument Performance Data (IPD), Run Monitoring, or Storage and Analysis mode, you can do so at any time.

In addition, we are continually reviewing and updating our security best practices to safeguard your data and the services we provide. We are ISO 27001 certified, which has a direct emphasis on international compliance and governance. Please review our security and data privacy whitepaper (Link) to learn more about our security practices.

We hope this makes your use of our SaaS products much easier. As always, please contact us at informatics@illumina.com if you have any questions.

QB#6005

Enhanced Run Monitoring in BaseSpace™ Sequence Hub

The ability to monitor sequencing runs in real time helps users identify issues that prevent costly sequencing errors. Many users rely on the Sequencing Analysis Viewer (SAV) to access detailed quality metrics generated by the real-time analysis software on Illumina instruments.

BaseSpace Sequence Hub has enabled users to remotely monitor their sequencing runs with the Run Charts function with a very similar interface to that of SAV. We have recently released a synchronized update with SAV to offer an expanded set of metrics for monitoring run quality. At the same time, we have added a few capabilities previously only present in SAV. These enhancements provide a consistent experience and enable users to make informed decisions on the quality of their sequencing runs – whether they are standing in front of their instrument accessing SAV or monitoring the run remotely using BaseSpace Sequence Hub.

Expanded menu of metrics that maintains consistency with SAV

BaseSpace Sequence Hub now includes per cycle Phasing and Pre-phasing metrics, % No Call, and Median QScore measures in the Charts section of Run Monitoring. These measures were also released as part of SAV 2.4.5. % No Call & Median QScores are available for all sequencing platforms. The new Phasing/Pre-phasing metrics are available for all platforms except MiSeq and HiSeq 2000/2500.

expanded menu.png

Traditional Phasing (and pre-phasing) metrics, which were calculated once at cycle 25, are now listed as “Legacy Phasing Rate.” The new per-cycle weights are listed as “Phasing Weight” in the Run Charts.

traditional phasing.png

Improved usability

The Charts section of Run Monitoring now includes the same menu structure as SAV 2.4.5. Now, metrics in the drop down menus only appear if they are available for the cycle, significantly improving the usability of the charts.

Extracted, Called, and Scored cycles have a minimum-maximum range

Run Monitoring now provides Extracted, Called, and Scored cycles as a minimum-maximum range during an instrument run. Previously, Run Monitoring showed only the maximum cycles. A wide spread between the leading and lagging tile might be an indication of a run problem. Now users can easily spot a problem with their run on both SAV and BaseSpace Sequence Hub.

New Metrics in Both SAV and BaseSpace Sequence Hub

In addition to the changes enumerated above, both SAV and BaseSpace Sequence Hubnow include Occupied Count (K) and % Occupied measures in the Charts section of Run Monitoring for NovaSeq systems. The Occupied Count is a measure of the number of wells on the flow cell with DNA. Adding these new metrics will help users understand their loading concentrations and identify issues with their sequencing run.

new metrics

 

For Research Use Only. Not for use in diagnostic procedures.