Reducing Genome Assembly Complexity with Optical Maps
نویسندگان
چکیده
De Bruijn graphs provide a framework for genome assembly, where the correct reconstruction of the genome is given by one of the many Eulerian tours through the graph. The assembly problem is complicated by genomic repeats, which allow for many possible Eulerian tours, thereby increasing the de Bruijn graph complexity. Optical maps provide an ordered listing of restriction fragment sizes for a given enzyme across an entire chromosome, and therefore give long range information that can be useful in resolving genomic repeats. The algorithms presented here align contigs to an optical map and then use the constraints of these alignments to find paths through the assembly graph that resolve genomic repeats, thereby reducing the assembly graph complexity.
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