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Gaithersburg, MD, United States

Patent
OpGen | Date: 2014-03-14

The invention generally relates to optical maps and particularly to computationally tractable methods of assembling large numbers of single molecule maps by dividing the maps into smaller groups of maps within which all of the maps are similar to one another by some metric. For each group, all of the maps are assembled into contigs. The resulting contigs are then assembled into one or more genome assemblies. By dividing the maps into groups, a number of comparison operations required for assembly is reduced and, since each group of maps can be assembled into a contig in a discrete operation, the overall assembly operation can be parallelized.


Patent
OpGen | Date: 2014-12-08

The present invention generally relates to devices and methods for immobilizing nucleic acids on a substrate. In certain embodiments, devices of the invention include a voltage source, and a substrate coupled to the voltage source, in which hydrophobicity of the substrate changes in response to an applied electric field and a surface of the substrate is coated with a substance that retains nucleic acids.


Patent
OpGen | Date: 2014-03-14

The invention generally relates to sequence assembly and particularly to ordering the alignment of contigs to reference maps. The invention provides systems and methods for assembling contigs by aligning those contigs to a reference map in descending order of placement confidence. Each placement decreases the number of possible placements for the remaining contigs, which otherwise would have been likely to match in numerous places. Contigs are thereby placed along the reference genome with confidence and thus can be assembled into a genome-scale sequence assembly.


The invention generally relates to systems, cartridges, and methods for automated characterization of a nucleic acid molecule, in particular, optical mapping of DNA from an organism. In certain embodiments, the invention provides a cartridge for characterizing a nucleic acid molecule, the cartridge including a reaction chamber having a derivatized bottom surface, at least one reagent reservoir, and a pump, in which the reaction chamber, the reagent reservoir, and the pump are fluidically connected to each other.


The invention generally relates to methods and kits for isolating nucleic acids from an organism. In certain embodiments, methods of the invention involve contacting a plurality of lytic enzymes to an organism, thereby lysing a cell wall of the organism to release the nucleic acid, and introducing at least one agent to separate the nucleic acid from the lysed cells, thereby isolating the nucleic acid.

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