Align. Compare. Confirm.

Current technologies break DNA into thousands of pieces to be sequenced and then reassembled, comparing the pieces to a published reference. But this process is time-consuming and costly. And comparing the small pieces to a reference genome presents challenges–the known high rate of misassembly and gaps in published reference sequences. OpGen’s technology provides a complete structural view that enables rapid assembly, and highly accurate order and orientation of the sequence contigs.

Whole Genome Maps–A More Accurate Approach

Long, intact single molecule DNA is analyzed in high definition, while maintaining the genome’s integrity (Figure 1). This novel  approach gives you a complete blueprint of the genome– accurate visual information, including  important positional changes that sequencing alone cannot detect.

Figure 1. DNA molecules are stretched out in a reaction card and processed. The single molecule are imaged, analyzed and represented as a barcode. 

You can take advantage of OpGen’s powerful technologies by contacting MapIt® Services or bring the the Argus® Whole Genome Mapping System into your lab. Learn more about Whole Genome Mapping technology–and how you can get faster, more accurate data for sequence assembly and public health epidemiology applications today.

News, Events, Updates

New white papers discuss solutions for common sequence assembly problems:

1. High cost and time required to finish and validate microbial genomes
2. The “Genome Assembly Problem”–now a solution for larger genome projects

“Using Whole Genome Mapping to Lower Cost and Reduce Time of Microbial Genome Assembly”

“Whole Genome Mapping Provides a Fast and Highly Accurate Solution to the Genome Assembly Problem”

 OpGen workshop showcases latest project updates at Plant and Animal Genome Meeting. Completed plum sequence and additional plant and animal projects in progress use Genome–Builder™ computational tools for faster, more accurate assembly of reference genomes. (OpGen’s Whole Genome Mapping System and Genome-Builder™ Software Suite Featured at the International Plant & Animal Genome XX Conference)

OpGen announces additions to management team and skills to support commercial expansion and growth in new markets. (OpGen Strengthens Management Team to Accelerate Commercialization Strategy)

You are invited! Join the discussion at OpGen’s Community.  Tell us what projects you’re working on, your challenges, your success. We want to hear what you are thinking and how we can help improve your reserach.

Faster Assembly Completion

Genome-Builder offers a completely new workflow for larger genome projects. This unique suite of computational modules delivers a new benchmark for completed plant, animal and human studies (Oct 14 Press Release). 

Reference genome projects can be very expensive, based on the significant number of downstream workflow steps and time. Genome-Builder combines your sequence data and single molecule DNA data to align and join gaps–you can eliminate downstream finishing steps, enabling a new, faster and less expensive approach to accurate completed projects (Figure 1).

 Figure 1: Genome-Builder joins sequence gaps without additional
workflow steps

Now you don’t have to settle for draft genomes that contain a high number of sequence gaps–or commit months or years to downstream workflow steps. Genome-Builder correctly joins sequence scaffolds, even in difficult to sequence regions containing centromeres with highly repetitive sequences. 

You can start improving your de novo reference genome projects now. Contact OpGen’s MapIt® Service to discuss a custom project plan, or bring the Argus® Whole Genome Mapping System and Genome-Builder into your lab.

Genome-Builder webinar                                                                                      

The Whole Genome in High Definition

The complexity of the malaria genome presents challenges for use of genomics methods. Malaria drug resistance has been linked to genetic changes ideally studied with comparative genomics–but the known challenges have prevented practical use of these methods. This study describes using Whole Genome Mapping technology to bridge this gap, providing a fast, easy and inexpensive approach for detecting important variations in genomic architecture.

Researchers at Walter Reed used the Argus® Whole Genome Mapping System to compare four strains to the reference sequence (1).  Riley, et al., generated Whole Genome Maps of four strains of P. falciparum: two are commonly used for vaccine development (3D7 and FVO), one is drug sensitive (D6), and one has known resistance to multiple drugs (C235). Using comparative genomics analysis, the authors found a unique 70 kb insertion in the C235 strain, and are following up on the likely hypothesis that this region confers multi-drug resistance (Figure 1).

 

 Figure 1. Unique 70 kb insertion discovered in multi-drug resistant C235 strain

 The malaria genome contains 14 chromosomes, presenting significant challenges for sequence assembly and validation. This paper describes a new technology for studying malaria strains that can be widely adopted to increase the understanding of genetic variation to combat the disease. Riley’s group demonstrated practical use of this technology for studying malaria, producing high quality contigs spanning four P. falciparum genomes in six weeks for less than $1,000.00 per genome.

Learn more about Whole Genome Mapping and Capt. Riley’s paper in his recorded webinar.       View Webinar

FOOTNOTE

1. Riley, M.C., Kirkup, B.C., Jr, Johnson, J.D., Lesho, E.P. & Ockenhouse, C.F. Rapid whole genome optical mapping of Plasmodium falciparum. Malaria Journal 10, 252 (2011).

Accurate Assembly. Validated.

The error rate in published sequences is surprisingly high. These errors can lead to conclusions that are inaccurate based on incomplete and inaccurate references. Additionally, rapid mutation and genomic structure changes are difficult to determine based on reference guided assembly. OpGen’s de novo Whole Genome Mapping (WGM) technology provides a fast, accurate and highly reproducible validation method for reference quality genomes.

Reference Genome Errors–the Data

Sixteen genomes from Genbank were analyzed using Whole Genome Mapping. Only five genomes had no discrepancies between the deposited sequence and the de novo Whole Genome Map. The remaining eleven sequences showed deletions, insertions, inversions, and translocations, strongly suggesting incomplete sequence and assembly errors (highlights Table 1).

Technology Adopted by Recognized Sequencing Authority

OpGen and the Institute for Genome Sciences (IGS) are developing a database of reference quality microbial sequences. “We are using this technology for validation of our de novo sequencing projects…the maps will serve as an extraordinary set of reference organism templates to be used by the large number of resequencing efforts worldwide,” commented Claire Frasier-Liggett, PhD, Director of IGS and Professor Medicine, Microbiology and Immunology at the University of Maryland School of Medicine.

OpGen’s Whole Genome Maps can provide a new standard for genome assembly and finishing, available through MapIt™ Services or bring the technology into your lab with the Argus™ Whole Genome Mapping System.

Learn more about our Whole Genome Mapping technology for sequence assembly and epidemiology applications.