Bionano Genomics Saphyr Genome Imaging Instrument
Bionano's Saphyr instrument provides genome mapping with unmatched structural variation detection and hybrid scaffolding capabilities

Structural Variation Discovery Platform

Resolve large-scale structural variations missed by next-generation sequencing (NGS) systems

Large structural variations are responsible for many diseases and conditions, including cancers and developmental disorders. Optical genome mapping with Saphyr detects structural variations ranging from 500 bp to megabase pairs in length and offers assembly and discovery algorithms that far outperform sequencing-based technologies in sensitivity.

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Saphyr sensitivity table

For mosaic samples or heterogeneous cancer samples, Saphyr detects all types of structural variants down to 1% variant allele fraction. Saphyr provides this performance typically with a false positive rate of less than 2%. Saphyr also calls repeats and complex rearrangements.

Detect large-scale structural variations for genetic disease, cancer, and cytogenomics.

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Optical Genome Mapping Provides Enhanced Speed and Throughput

Rapid optical genome mapping using whole genome imaging for human research applications

Saphyr features enhanced optics with adaptive loading of DNA utilizing machine learning. The Saphyr Instrument and high-capacity Saphyr Chip® combine to deliver genome maps at the speed and scale your research demands.

  • Long molecules from 150,000 bp to multi-megabase pairs
  • 15 Tbp output per Saphyr Chip for human samples for deep structural variant discovery (5 Tbp per flowcell of molecules larger than 150 kbp)
  • Sample to structural variation call or genome scaffolding in as little as 4 days
Bionano Genomics Chip - Flow Cell

Simplified Workflow

Optical genome mapping automation features and intelligent sample preparation simplify the process

Saphyr optical genome mapping offers automated features that minimize hands-on time.

  • Requires less than 3 minutes hands-on instrument time per chip
  • Automatic optimization of run conditions based on sample characteristics maximizes throughput
  • Saphyr Chip Clip protects sample integrity and eliminates the need for instrument wash cycles between runs


Optical genome mapping automation features and intelligent sample preparation simplify the process

Saphyr runs each genome in its own flow cell. Each Saphyr chip holds three flow cells, and 100x coverage of 3 human genomes is collected in less than 6 hours. That means 12 human samples at 100x coverage per day, or up to 96 per week.

For cases requiring higher coverage, like mosaic samples or heterogeneous tumors, the run can be extended up to 24 hours to collect as much as 400x coverage of a human genome for each of the three flowcells.


Bionano Genomics Saphyr Genome Imaging Instrument


Saphyr Assure

Remote quality control ensures maximum performance at all time

The Saphyr Assure Service provides an optional (opt-in required) automated health monitoring feature that continuously inspects data quality and instrument performance. Performance issues are detected before data quality and performance are impacted allowing Bionano Support to proactively repair the system with minimal downtime.

Intelligent Data Solutions

Automate data analysis—monitor and manage the Saphyr Instrument remotely

The Bionano suite of hardware and software for Saphyr streamlines your workflow and reduces time to result. Learn more about Bionano Data Solutions.

Bionano Genomics Saphyr System

Sample Preparation Kits

Extract high-molecular-weight DNA for human, plant and animal genome mapping

The Bionano Prep DLS DNA labeling kit provides all the enzymes, dyes and buffers you need to label non-amplified DNA for Saphyr. Controls for validating the labeling biochemistry are also provided. Learn more about Bionano Prep kits.

Saphyr Ordering Information and Brochure


  • Saphyr System with Bionano Access Server: Catalog #90023
  • Saphyr Compute Server: Catalog #80013
  • Saphyr Chip G2.3* : Catalog #20366
  • Saphyr Chip G2.2* : Catalog #20367
  • Bionano Compute Server: Catalog #80014

*Compatible only with Saphyr System #90023 (Saphyr Instrument #60325)


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