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P5: Reducing Genome Assembly Complexity wit Optical Maps

Author: Lee Mendelowitz , Advisor: Mihai Pop (CS and CBCB)


Problem Statement Presentation

Project Proposal

Abstract

De Bruijn graphs provide a framework for genome assembly, where each Eulerian trail through the graph corresponds to a possible reconstruction of the genome. The assembly problem is complicated by genomic repeats, which introduce many alternative possible reconstructions and increase the complexity of the de Bruijn graph. Optical maps provide an ordered listing of restriction fragment sizes for a particular 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 use this information to find paths through the assembly graph that can resolve genomic repeats, thereby reducing the assembly graph complexity.



MidYear Progress Report and Presentation

Final Presentation , Final Report