Dissertation Defense – Ian Fiddes (BME)
Mon Nov 20, 2017 11:30am – 2:30pm Pacific Time
Location: BE-330, Engineering

The recent introductions of low-cost, long-read and read-set sequencing technologies coupled with intense efforts to develop efficient algorithms have made affordable, high-quality de-novo sequence assembly a realistic proposition. The result is an explosion of new, ultra contiguous genome assemblies. To compare these genomes we need robust methods for genome annotation. I describe Comparative Annotation Toolkit (CAT), an annotation pipeline which provides a flexible way to simultaneously annotate entire clades and identify orthology relationships. I show that CAT can be used to improve annotations on the rat genome, annotate the great apes, annotate a representative set of mammals, and annotate personal human genomes. I demonstrate the resulting discovery of novel genes, isoforms and structural variants and how these annotations greatly improve cross-species RNA expression experiments.