Bionano Genomics Saphyr Genome Mapping Technology
Bionano Genomics Saphyr Genome Mapping Technology

Saphyr Workflow

Image extremely long, high-molecular-weight DNA for analysis with Saphyr’s streamlined workflow.

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Saphyr Workflow

Sample Preparation

Bionano sample preparation kits provide everything needed to isolate ultra-high molecular weight DNA from fresh or frozen blood, cultured cells, and plant and animal tissues.

Unlike standard DNA isolation methods such as precipitation, column, or bead-based methods, which yield reads too small and fragmented for assembly, Bionano’s sample prep method produces the large molecules, greater than 150 kbp, needed for assembly.

Bionano provides two methods to isolate ultra-high molecular weight DNA that is compatible with Saphyr: a solution-based method called Bionano Prep SP, and a method based on agarose gel plug DNA isolation.

This Bionano Prep SP Blood and Cell Culture DNA Isolation Kit can provide ultra-high molecular weight DNA in less than 4 hours for EDTA-collected blood and mammalian cell cultures. It utilizes a lyse, bind, wash, and elute procedure that is common for silica-based DNA extraction technologies in combination with a novel paramagnetic disk. Unlike magnetic beads and silica spin columns, which shear large DNA, the Nanobind Disk binds and releases DNA with significantly less fragmentation.

For ultra-high molecular weight DNA isolation from plant, animal and human tissues, detailed protocols  are provided to users. These protocols are based on the isolation of cells or nuclei in an agarose matrix, where DNA purification takes place while the molecules are stabilized in agarose. By the end of the purification process, the agarose is digested and molecules up to chromosome arm lengths in size are released.

Learn more about Bionano DNA Isolation Kits and Reagents.


The Bionano DNA labeling kit provides the reagents needed to label DNA at specific sequence motifs for imaging and identification. These labeling steps result in a uniquely identifiable sequence-specific pattern of labels to be used for de novo map assembly.

Sample Labeling

Bionano has two labeling chemistries, one using our newest Direct Labeling chemistry and a predecessor based on nicking endonucleases.

The primary chemistry, Direct Label and Stain (DLS), recognizes a 6 basepairsequence motif and transfers a fluorescent label directly to it in a single enzymatic step.

The predecessor chemistry is the nickasebased labeling, Nick-Label-Repair and Stain (NLRS). A nicking endonuclease creates a single-strand nick in the long DNA molecules at a specific recognition site, followed by incorporation of fluorescently labeled nucleotide analogs.NLRS chemistry leverages many commercially available enzymes to provide greater flexibility of target sequences.

Learn more about DNA Bionano labeling kits.

Linearization and Imaging

A labeled DNA sample is pipetted onto the Saphyr Chip™ in one of the flowcells. Saphyr electrophoretically controls the movement of DNA in the flowcell. A gradient of micro- and nano-structures, upstream of Saphyr Chip’s NanoChannels, gently unwinds and guides DNA into the NanoChannels.

Bionano Saphyr Chip Schematic
Bionano Saphyr Chip Schematic
Bionano Saphyr Chip Schematic

Saphyr Chip’s NanoChannels allow only a single linearized DNA molecule to travel through while preventing the molecule from tangling or folding back on itself. The nanofluidic environment allows molecules to move swiftly through hundreds of thousands of parallel NanoChannels simultaneously, enabling high-throughput processing to build an accurate Bionano genome map.

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Once the DNA is stretched inside the NanoChannels, the high-resolution Saphyr camera images them. Long molecules spanning beyond a field of view are stitched together. Once imaged, the molecules are flushed and the process is repeated, enabling imaging of more than 25 Gbp of DNA per hour per flowcell.


Once raw image data of labeled long DNA molecules is captured by the Saphyr instrument, it is converted into digital representations of the motif-specific label pattern. Bionano Solve™ data analysis software then assembles the data de novo to recreate a whole genome map assembly.

Bionano genome maps enable a variety of analyses, including hybrid scaffolding and structural variation detection. Next-Generation Sequencing (NGS) analyses often rely on alignment of short reads to a reference to infer the underlying genome structure. With this strategy, the ability to decipher regions where the reference itself is incorrect or significantly different from the genome of interest is lacking. Bionano assemblies are not guided by a reference, allowing for unbiased reconstruction of the genome structure.

Learn more about Bionano Data Solutions.


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