Browsing by Author "Walve, Riku"

Although recent developments in DNA sequencing have allowed for great leaps in both the quality and quantity of genome assembly projects, de novo assemblies still lack the efficiency and accuracy required for studying individual genomes. Thus, efficient and accurate methods for calling and genotyping structural variations are still needed. Structural variations are variations between genomes that are longer than a single nucleotide, i.e. they affect the structure of a genome as opposed to affecting only the content. Structural variations exist in many different types. By finding the structural variations between a donor genome and a high quality reference genome, genotyping the variations becomes the only required genome assembly step. The hardest of the structural variations to genotype is the insertion variant, which requires assembly to genotype; genotyping the other variants require different transformations of the reference genome. The methods currently used for constructing insertion variants are fairly basic; they are mostly linked to variation calling methods and are only able to construct small insertions. A subproblem in genome assembly, the gap filling problem, provides techniques that are very applicable to insertion genotyping. Yet there are currently no tools that take full advantage of the solution space. Gap filling takes the context and length of a missing sequence in a genome assembly and attempts to assemble the sequence. This thesis shows how gap filling can be used to assemble the insertion variants by modeling the problem of insertion genotyping as finding a path in de Bruijn graph that has approximately the estimated length of the insertion.