Hierarchical assembly of optical maps
AssigneeOpgen, Inc.
InventorDeacon John Sweeney
Life of this patent
Estimating the term…
Abstract
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.
Claims25
A method of obtaining genomic information, the method comprising:
- generating a plurality of single molecule optical maps from a nucleic acid sample;
- linking pairs of the maps according to a similarity metric;
- dividing the plurality of maps into groups comprising linked maps;
- assembling the linked maps within each group into a contig to produce a plurality of contigs;
- and
- assembling the plurality of contigs into at least one genome assembly.
A method of obtaining contigs, the method comprising:
- generating a plurality of single-molecule ordered restriction maps from a nucleic acid sample;
- segregating the maps into a plurality of groups, each group comprising a plurality of linked maps linked by a similarity metric;
- and
- assembling the linked maps within each group into a contig to produce a plurality of contigs.
Dependencies are inferred from the claim text.