Opgen Argus

The Opgen Argus is one of a group of machines for optical mapping. Optical mapping delivers ordered, whole-genome restriction maps from single DNA molecules. High molecular weight DNA needs to be prepared for the system, and consequently DNA extraction is a critical part of the workflow.

DNA molecules are flowed through microfluidic channels and immobilised on a charged surface, this is then digested with a restriction endonuclease. The order of the fragments is maintained, and then DNA fragments are stained with a dye which fluoresces. The signal is proportional to the fragment length. Genome assembly is done by overlapping fragment patterns of the larger molecules from which they were derived.

Having higher-order structural information about a genome is very helpful for genome assembly work, allowing you to size gaps and act as ‘super scaffolds’ for fragmented assemblies from next-generation sequencing platforms. The system can be used to polish existing assemblies, create de novo assemblies, used for comparative genomics or strain typing. The throughput of the Argus means it is suitable for microbial genomes.

The optical system means that the read lengths can be 150kb to 2Mb and approximately 45,000 optical reads are generated per run, which gives a throughput of approximately 13Gb in 3 hours.

We have used the Opgen for strain typing studies and validating microbial assemblies from short-read NGS platforms, but it is also a great platform for quality control of high-molecular weight DNA, enabling you to understand the size distribution of fragments when a gel-based system can no longer resolve fragments.