Strand NGS v2.7 Released

We are happy to share the release of Strand NGS v2.7. This new version comes with several exciting features and enhancements. Below is the summary of few key features and enhancements made in this release. For more details, please refer to the release notes.

Low frequency SNP detection:

Normal cell contamination in tumor samples is a common phenomenon that results in low supporting reads for a variant. A similar scenario is also encountered while detecting variants in non-diploid organisms. The limit of detection for germline SNP caller is typically 8% whereas with the newly introduced low frequency caller, variants with supporting reads as low as 2% can also be detected. In addition, carefully designed pre-packaged SNP filters can further flag likely false positive variants, thus allowing the users to focus only on high confidence variants.

Split Read Realignment:

Split read realignment (SRR) aims to realign poorly aligned reads by considering other split reads in the vicinity, thereby increasing the support for low frequency structural variants (SVs). Using data from a clinical sample, we demonstrated the applicability of this approach by detecting a EML4-ALK gene fusion event which had low supporting reads before realignment.

Support for circular genome:

Alignment of reads from circular genomes is now fully supported through enhancements made to our existing split alignment feature. In the previous versions, reads spanning the boundaries were poorly aligned resulting in false insertions. In an Escherichia coli data set, using these enhancements, most of the reads at the boundary are now properly aligned. These reads were originally either unaligned or poorly aligned with large insertions.

Targeted VAL creation:

Annotating variants with information from external sources such as dbSNP, COSMIC, etc is typically a time consuming step due to the large size of the annotation databases. A script is provided with this release to create a subset of the annotations based on targets of interest. This targeted VAL can then be used instead of the original annotation database to annotate variants. Depending on the size of the target panel, a reduction of ~95% in time is expected.

Update to Java 1.8:

In our latest version, we have updated the code to work with Java1.8. As a result of this upgrade, El Capitan version of MacOS is now supported.

All these new features are available once you update the product by clicking on Update Product from the Help menu. Many of the improvements made in this release are based on your valuable feedback. We look forward to your continued support.

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