Qualifying Examination: Overlap graph-based sequence assembly in bioinformatics

This is my qualifying examination final report and presentation for the oral exam, presented at Michigan State University on August 29th. It reviews how the genome assembly problem formulation changed since the foundation of genome sequencing, with special attention to overlap graph-based sequence assembly. Three assemblers implementing this theoretical framework are reviewed, and a fourth one based on de Bruijn graph serves as a comparison between shared methods and differences on each approach. Finally possible directions for future works are discussed.