Bionano Genomics Saphyr System
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. 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 5% Variant Allele Fraction. Saphyr provides this performance typically with a false positive rate of less than 2%. Saphyr also calls repeats and complex rearrangements.

Enhanced Speed and Throughput

Rapid optical 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
  • 3900 Gbp throughput per Saphyr Chip for human samples for deep structural variant discovery (1300 Gbp per flowcell of molecules larger than 150 kbp)
  • Sample to structural variation call or genome scaffolding in as little as 5 days
Bionano Genomics Saphyr System

Simplified Workflow

Automation features and intelligent sample preparation simplify the process

Saphyr 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

Flexible Mapping Options

High throughput and lower cost per sample allow for a wide range of experiment design options

Generate high-resolution physical genome maps with greater speed and coverage at a lower cost. Saphyr can run most genomes in a single flowcell, in just 12 hours. With Saphyr Chip’s three-flowcell design, you have the power to process up to 6 human samples at 100x coverage per day, or 42 per week.

For cases requiring higher coverage, like mosaic samples or heterogeneous tumors, the run can be extended up to 48 hours to collect as much as 400x coverage of a human genome for each of the three flowcells.


Bionano Genomics Saphyr Instrument

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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