Structural variation in genomics is a challenging task. To detect inversions, large deletions (by ‘large’ this is generally defined to be anything more than 50 bases or so), large insertions, and translocations in the genome takes a lot of creative alignment algorithms and hard work. Also you need to orthogonally verify each variant call, a difficult and time-consuming task.
Alternative Technologies for SV Detection
Long-read technologies (Pacific Biosciences, Oxford Nanopore) is one way to tackle this challenge, but the alignment algorithms to make these calls pose their difficulties in accuracy and computational overhead. Virtual long read technologies (BGI/MGI’s Long Fragment Read technology, Illumina’s abandoned Moleculo technology, Dovetail / Phase Genomics / Arima Hi-C technology) is another approach. Optical, single-molecule approaches is yet another, including BioNanoGenomic’s Saphyr, of which you can add Nabsys.
Nabsys 2.0 is a relaunch of a technology first highlighted here in 2014. After closing down operations and reorganizing under a new entity Nabsys 2.0 LLC, at last October’s ASHG conference in San Diego they showcased their new platform, called the Nabsys HD-Mapping platform.
List of applications
Their application summary lists De Novo map assembly, Structural Variant discovery, Variant verification, Metagenomics, Hybrid assembly, and Strain identification. For additional details you can access their webpage here.
For background, they have put on the BiorXiv preprint server a manuscript of the technology applied to mapping dated May 2017, entitled “High-Definition Electronic Genome Maps From Single Molecule Data”. A second preprint is this manuscript published a few days later also in May 2017 titled “Automated Structural Variant Verification In Human Genomes Using Single-Molecule Electronic DNA Mapping”. I find it a little strange that either manuscript have not made their way into print yet.
More data from Nabsys 2.0 at #ASHG18 and upcoming #AGBT19
At the Society for Human Genetics conference last October, they had reprints of this poster “High Throughput Validation of NGS Structural Variant Calls using High Definition Mapping” (PDF). It is clear from this link that they will be exhibiting at #AGBT19 and will be presenting two posters there, so stay tuned for additional updates!