OpGen > Technology & Applications > Sequence Assembly

Sequence Assembly

One Genome. One Image.
The Answers Are Right Before Your Eyes.

Whole Genome Mapping simplifies genomics research with a high definition view of the entire genome. The result is an ordered picture that provides the answers you need to accelerate your assembly and comparative genomics projects–and with more confidence in the accuracy of the data.

  • Compare multiple Whole Genome Maps and related isolates
  • Find differences in the maps
  • Look at annotated genes in the sequence that align to the different areas


Sequence contigs (top) are aligned to Whole Genome Map (top-center) to orient contigs and identify misassemblies. Contig alignment and gap length measurement (lower panel) enable faster and more accurate finishing.

Improving Genome Sequence Assembly (<100Mb)

Genome assembly is a computational challenge. Contig order, gaps and repetitive regions are known problems, and additional finishing with libraries is expensive. Whole Genome Maps added to assembly workflows provides finished assembly in twenty-four hours–de novo assembly or maps used as a reference scaffold for accurately orienting sequence contigs.

Single-molecule Maps Complete Large Genomes (>100 Mb)

DNA assembly for larger genomes (>100 Mb) presents even more challenges–size and complexity of the sequence, downstream finishing and significant bioinformatics required. OpGen’s new Genome-Builder™ software improves sequence assembly in plants, animals and human genomes. With as little as one to two weeks for assembly, potentially 90% of scaffold gaps may be joined without BAC libraries, fosmids and extensive resequencing.

Comparative Genomics at a New Level

Even the best sequencing efforts can result in sequence gaps, assembly errors and structural changes that go undetected. These challenges compromise the detection and understanding of differences between similar genomes. The linear and visual nature of Whole Genome Maps provides a highly accurate and reproducible method for detecting these differences between strains and species.

Align: Our Whole Genome Map provides a scaffold for easier, more accurate genome assembly—simplifying the alignment and ordering of contigs.

Compare: The differences between strains and species are quickly and easily seen with Whole Genome Maps. Chromosomal rearrangements such as insertions, duplications, deletions, and inversions are readily identified in a single glance.

Confirm: Accurate genome assemblies are confirmed and misassemblies and gaps identified through alignment with our Whole Genome Map.

“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

“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

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