UC Santa Cruz

In this work, I first describe methods for ONT assembly phasing, using parental information. Second I outline the differences in long read methylation calling technologies in regards to how they may still be used for differential analysis across technologies. In the third chapter, I outline a methylation analysis framework as a part of a Nanopore-only pipeline for phased methylation calls, assembly, small, and structural variants. Finally, I present an analysis of the impact of structural variants on gene expression and methylation in a dataset of hundreds of prefrontal cortex brain tissue samples from the National Institute of Health's Center for Alzheimer's and Related Dementias (NIH CARD).