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.

  • 99% sensitivity for homozygous insertions/deletions larger than 500 base pairs
  • 95% sensitivity for heterozygous insertions/deletions larger than 500 base pairs
  • 95% sensitivity for balanced and unbalanced translocations larger than 50,000 base pairs
  • 99% sensitivity for inversions larger than 30,000 base pairs
  • 97% sensitivity for duplications larger than 30,000 base pairs
  • 97% sensitivity for copy number variants larger than 500,000 base pairs

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 ideal 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 100,000 bp to megabase pairs
  • 640 Gbp throughput per Saphyr Chip per day for human samples for deep structural variant discovery (320 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 Worfklow

Automation features and intelligent sample preparation simplify the process

Saphyr offers automated features that minimize hands-on time, while upgradable components ensure Saphyr delivers value over the long term.

  • 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 one day. With Saphyr Chip’s dual-flowcell design, you have the power to generate two independent maps from one sample, with two enzymes, and combine the data.

  • Improve contiguity of sequence assemblies even more than with single enzyme scaffolding
  • Use the two maps generated per chip to correct assembly errors with greater accuracy

The two flowcells can run entirely unrelated samples as well, allowing you to map two genomes in a single 24 hour run.

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

Bionano reagent kits supplement readily available enzymes, with 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 Instrument: Catalog # 90001Bionano Genomics Saphyr Brochure
  • Saphyr Compute Server: Catalog # CR-002-01
  • Saphyr Chip: Catalog # FC-030-01
  • Saphyr Chip Clip: Catalog # FC-031-01



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