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Workflow

Mapping Genomes in 4 Steps

The Argus® Whole Genome Mapping System and MapSolver™ analysis software provide a straightforward, automated workflow for evaluating whole genomes and chromosomes in as little as 24 hours for smaller genomes.

1. Extract

Using OpGen’s optimized DNA extraction kit, high molecular weight DNA needed to produce Whole Genome Maps can be extracted in as little as two hours.

2. Immobilize & Digest

Single DNA molecules are flowed through microfluidic channels and immobilized on a charged glass surface. The immobilized DNA is digested, maintaining the fragment order.

Genomic DNA, captured as single DNA molecules from random breakage of intact chromosomes, is loaded into microchannels, immobilized electrostatically, then digested with a restriction endonuclease.

Digestion reveals cleavage sites. The restriction fragment order is maintained for each molecule.

3. Measure & Assemble

The DNA fragments are stained with fluorescent dye; fragment length is proportional to fluorescence intensity. By overlapping fragment patterns, the single-molecule maps are assembled to produce a Whole Genome Map that provides a minimum 30 X coverage.

Automated measurements capture fluorescence intensity to determine fragment sizes.

Overlapping Single-molecule Maps are assembled to produce a highly accurate, Whole Genome Map. The red circle indicates 30x coverage, ensuring accuracy of the consensus Whole Genome Map.

4. Analyze

The MapSolver™ Analysis tool provides powerful features to evaluate and compare Whole Genome Maps. Discover genetic variation, perform high-resolution epidemiology, or accelerate whole-genome sequencing.

View and compare genomes
Identify important genetic variations
Upload sequence contig data to align contigs against an ordered whole-genome scaffold
Use the Whole Genome Map as an independent source to guide sequence placement, confirm assemblies, identify misassemblies and gaps, and finish de novo sequences

Directly compare maps to discover insertions, deletions, and other genetic elements that other technologies miss. Differences and similarities are highlighted for at-a-glance discovery.

Map-based similarity clustering accurately distinguishes strains and describes relatedness between isolates.

Align sequence contigs with Whole Genome Maps to quickly orient contigs, locate gaps and correct misassemblies.

“Physical map and genetic map still should be emphasized as an important parts of a reference genome. Recent progress in technologies, such as the whole genome mapping high-throughput platform offered by OpGen, now provide the tools for efficient physical map construction. This independent technology provides not only the validation of the genome sequencing, but also provides the large-scale chromosome structure information that cannot be detected by sequencing. We applied this technology as an assistant tool of the NGS to assemble bacterial, plant and large mammalian genome with reliable accuracy and generate the sub-chromosome graded assembly. The experience in these genome assembly projects shows that the physical map should be the standard for any reference genome to be assembled in further.”

Xun Xu, Ph.D.

Deputy Director at BGI

This independent technology provides not only the validation of the genome sequencing, but also provides the large-scale chromosome structure information that cannot be detected by sequencing.

Xun Xu, Ph.D.
Deputy Director at BGI

“Our research focuses on a wide variety of projects from viruses and microbes to crop plants and mammals. Many of our projects are de novo assembly projects, where, without a closely related genome sequence, it can be difficult to critically assess the results. We often combine different sequencing technologies, and we are finding that regardless of the sequencing platform, error correction, or assembler used, OpGen’s Whole Genome Mapping identifies misassemblies and provides the highest quality de novo assembly for further research.”

Matthew Clark, Ph.D.

Team Leader, Sequencing Technology Development

The Genome Analysis Centre (TGAC), Norwich, UK

OpGen’s Whole Genome Mapping identifies misassemblies and provides the highest quality de novo assembly for further research.

Matthew Clark, Ph.D.
Team Leader, Sequencing Technology Development

“We adopted OpGen’s Argus System as the most advanced way of adding Whole Genome Mapping to improve whole genome sequences. We combined Whole Genome Maps with sequence assemblies to correct errors and misassemblies in bacterial genome sequences as part of our program in the Human Microbiome Project. We are now moving the technology into larger genome projects.” 

George Weinstock, Ph.D.

Associate Director  The Genome Institute at Washington University

We combined Whole Genome Maps with sequence assemblies to correct errors and misassemblies in bacterial genome sequences. This is part of our program from the Human Microbiome Project.

George Weinstock Ph.D.
 Associate Director 
The Genome Institute at Washington University

“Certain things you just have a tough time answering with de novo sequencing. And assembly doesn’t always work out as sweetly as you would like. So definitely for any whole genome de novo project that people are insistent on closing we would do a Whole Genome Map optically as well as de novo assembly. And the amount of money you would save is in the thousands of dollars in finishing.”

Stefan Green

Director of DNA Services

University of Illinois Chicago Research Resources Center (UIC RRC)

Definitely for any whole genome de novo project that people are insistent on closing we would do a Whole Genome Map.

Stefan Green
Director of DNA Services