Optical Mapping
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Optical Mapping
An Optical Map is a high-resolution, ordered, whole genome restriction map generated from single DNA molecules extracted from bacteria, yeast, or other fungi. Optical Mapping is a novel technology with unique capabilities in the field of microbiology, with specific applications in the areas of Comparative Genomics, Strain Typing, and Whole Genome Sequence Assembly. Optical Maps are generated de novo, independent of sequence information, require no amplification or PCR steps, and provide a comprehensive view of whole genome architecture. An Optical Map is displayed in the MapCode pattern where the vertical lines indicate the locations of restriction sites, and the distance between the lines represent the restriction fragment size.


With Optical Mapping, you will be able to investigate microbial structure, function, diversity and genetics — without the need for amplification, PCR, cloning, paired-end libraries, pure isolates, or genomic specific reagents. Using OpGen’s unique de novo Optical Mapping Technology, the Argus Optical Mapping System, BGI delivers high resolution, ordered whole genome restriction maps from single microbial DNA molecules.


  1. Comparative Genomics
  2. Whole Genome Sequencing Assembly
  3. Strain Typing

Assisting Bacteria Genome Assembly - The Aacinetobacter baumannii Case


In this case, unordered contigs were aligned to the matching regions on the Optical Map. Alignment lines are drawn between compared Optical Maps to show placement. Crossing alignment lines indicate reverse orientation. The Gap sizes and locations (white colored) are visualized and enable further targeted analysis for whole genome closure.

Comparison of Assembly Performance Among Three Methods:

Method 2 combines optical mapping and Solexa reads assembly, bringing the number of scaffolds to 1. It works better than method 1 and 3 which use large and small fragments to assemble without Optical Mapping.

Method Number of scaffolds Scaffold total length Total length of outer gaps and inner gaps Contig length/ genome length (%)
Assembly (short library reads only) 88 4,060,072 309,996 85.88%
Assembly (short reads) + Optical Mapping 1 4,292,545 426,960 90.05%
Assembly (short reads + longer reads) 74 4,366,732 307,400 92.96%


  1. Enzyme digestion result
  2. Assembly and analysis
  3. Optical map
  4. Scaffold placement
  5. Comparative genomics
  6. Strain typing

Sample Requirements:

  1. Sample condition: Bacteria DNA with size≥150Kb
  2. Sample concentration: 5-10 DNA/ image

We suggest sending bacterial cultural plate. For bacterial cultural plate, two more control plates are needed for re-culture. Label the culture condition and pathogenicity.

For pathogenic bacteria, suggest sending Bacteria Plug.