Franklin keeps improving! We're proud to announce this latest version, which includes several updates that we expect will make its use easier and more helpful.
New features include:
New and Improved Whole Genome Viewer
As part of Franklin’s whole genome workflow improvements, we’re excited to launch a new and improved whole genome viewer that shows the entire genome in a single view.
Access to this viewer is through the top of the Workbench page. This view includes 3 tracks:
Coverage across the genome
Allele balance
Predicted copy number, as assessed by Rainbow, Franklin’s structural variant caller
You can also zoom in to view a specific chromosome by clicking on the chromosome number or selecting it on the menu.
This allows you to visualize the entire genome and help to identify large deletions, duplications, and even mosaic states.
In addition to the Whole Genome Viewer, we’ve also improved the CNV variant confidence visualization, now displayed in a single view with multiple tracks, significantly improving the ability to assess the variant’s raw data:
Coverage
A/B, showing the balance between heterozygous and homozygous variants
Predicted copy number, showing the predicted copy number calculated by Franklin’s own proprietary variant calling algorithm
Prediction score, showing the strength of the variant caller at that position.
Selection of the comparator samples is available using the small menu in the viewer header.
New Batch Quality Control
High-volume labs can now benefit from Franklin’s new QC Batch, which offers better ways to monitor and streamline the quality assurance and performance of whole sequencing runs, as part of the routine lab workflow.
The new batch allows you to:
Compile multiple samples into the same batch.
Generate and download a customizable Batch QC Report for the entire batch
View an RNA expression control QC metric
Explore control samples, which target known hotspots and verify the propriety of the VAF calling of the manufactured sample
Review dedicated thresholds for RNA expression on the Ampliseq focus targeting
Examine SNP profiling, which detects polymorphism in small VAF and occurs in other samples in the batch, in order to detect contamination
Observe a dedicated threshold for the number of reads per sample in comparison to the batch average, using a statistical abnormality model, in order to detect samples that were poorly sequenced
Using these new features not only will help you improve the quality control of your samples, but also optimize your protocol. For example, during a collaborative effort with our partners from the BC Cancer Agency, we implemented these new elements in the Ampliseq focus kit** workflow, creating an automatization of this test for future use. This process can easily be copied to other kits, such as TSO500, OCA PLUS, and more, according to each user’s needs and available resources.
** We wish to share our gratitude to Curtis Hughesman from the BC Cancer Agency for the development and validation of this kit.
Additional Improvements
Further improvements implemented in April 2022:
Somatic analysis improvements
Comments are now visible on the variant tile
Improved support for MSI on various panels, including TSO500
Sub-tiers supported on AMP classification
The sample variant track is now included on the confidence viewer
Transcripts versions have been updated
We hope you find these updates useful! We encourage you to give them a try and share your thoughts. We appreciate your feedback.
If you’re interested in learning more about these new features, or want to explore our new and improved reporting studio, feel free to schedule a call with us!
- The Franklin Team |