Reveal all classes of structural variants using Bionano’s optical genome mapping Stratys™ System. Explore the Stratysphere!

Achieve Unparalleled Structural Variant Detection

Routinely detect all classes of structural variants down to 500 base pair (bp) resolution and 5% variant allele frequency (VAF) with optical genome mapping (OGM) using the Saphyr™ system. Saphyr™ is the most powerful structural variant detection tool available, detecting genomic variants commonly missed by next-generation sequencing (NGS) technologies and conventional cytogenetic techniques.

Saphyr™ System Brochure

Explore the Saphyr system brochure to get an overview of the system, range of applications, workflow and more.


Empower your lab with advanced SV detection using optical genome mapping.

The Saphyr™ system provides optical genome mapping of ultra-high molecular weight (UHMW) DNA in its native state, from molecules 150 kbp to multi-megabase pairs in length.

In as little as three days, complete the entire workflow from sample to structural variation call using the Bionano sample preparation kits, Saphyr™ system, and software.

Achieve broad, unbiased genomic coverage with flexible data collection.

The genomic coverage achieved with the Saphyr™ system is flexible and allows for the detection of heterozygous variants or rarer variants found in mosaic samples and heterogeneous tumors.

Collect 100X coverage of a human genome in as little as six hours. See deeper and rarer variants by simply extending the data collection time on Saphyr™ at no additional consumables cost. Achieve 400X coverage in 24 hours and provide SV detection down to 5% VAF. Further extend runs to see even lower VAF.

Experience seamless integration and workflow using the Saphyr™ Chip® consumable and Saphyr™ system.

The Saphyr Chips utilize hundreds of thousands of massively parallel nanochannels that linearize long, labeled DNA molecules, allowing the Saphyr instrument to directly image your samples.

Sample loading on the Saphyr Chip is fast and easy. Pipet up to three samples into individual flow cells on the chip. Load up to two chips onto the Saphyr instrument per run for a maximum throughput of six samples per run.

The Saphyr instrument and chips leverage machine learning-based adaptive loading and automatic run optimization to ensure walk-away scanning and the fastest possible throughput for runs.

Ensure maximum performance with automated health system monitoring via remote access.

The Saphyr™ Assure Service provides an optional (opt-in) automated health monitoring feature that continuously inspects data quality and instrument performance. The feature detects issues before they effect data quality and performance so Bionano Support can proactively repair the system with minimal downtime.

Saphyr™ System Performance by Application

The performance details of Saphyr™ vary depending on the application and analysis pipeline used.

Application Germline DNA Analysis Cancer Analysis
Data collected 400 Gbp 1.5 Tbp
Coverage setting 100x 400x
Effective coverage 80x 300x
Variant allele frequency 50% >5%
Analysis pipeline De novo assembly Rare variant analysis
Performance (size) by variant type*
Insertions >500 bp >5 kbp
Deletions >700 bp >7 kbp
Stable Repeat Expansion / Contractions >500 bp >5 kbp
Duplications >30 kbp >150 kbp
Translocations >70 kbp >70 kbp
Inversions >30 kbp >70 kbp

*Performance shown is >90% sensitivity

Learn more about OGM

Read about what structural variations are and why they matter.

Learn More

See how OGM reveals structural variation in a way that has never been done before.

Learn More

Find the latest research in our Publications Library.

Learn More

Hear What Some of our Customers Say About Using the Saphyr™ OGM System in Their Research

“The Saphyr™ system is a very reliable analysis tool, impressively sensitive to detect different SVs.”

Arran Constantine

“OGM reveals more of what matters: more clinically relevant SVs leading to higher success rates and resolution of unsolved cases.”

Laila El-Khattabi
Hôpitaux de Paris (AP-HP)

“With OGM we are changing subjectivity to objectivity in going from a visual microscope-based karyotype to a high-resolution digital output.”

Adam Smith
University Health Network

Downloads and Resources

Speak to an expert, to learn more details on how OGM works and how it can fit the needs of your institution

Talk to a specialist

Related Products

Compute Solutions

Learn More

Sample Preparation Kits

Learn More

VIA™ Software 

Learn More