Degree Type

Dissertation

Date of Award

2014

Degree Name

Doctor of Philosophy

Department

Veterinary Microbiology and Preventive Medicine

First Advisor

Lisa K. Nolan

Abstract

Advancements in sequencing technology have driven an ever-growing body of genomic sequence data to new heights. Since publication of APEC O78 sequencing paper (Chapter 2) one year ago, sequencing technology has grown in leaps and bounds and has plummeted in price. The affordability of these systems and availability of sequencing services have made these technologies accessible to smaller laboratories, focusing on individual biological organisms and systems, such as our own lab with APEC. This `perfect storm' has made it feasible to sequence several of the APEC isolates in our collection. Although data generation is only the beginning, two substantial NGS bottlenecks for many labs are (1) closing and finishing the genomes to high quality standards and (2) taking the sequence data to biological insight and relevance, especially when the volume of data overwhelms paradigms for standard data analysis. This dissertation explores the process of sequencing and closing a diverse set of APEC genomes to finished quality, then creates a framework to complete a new programmatic pipeline and visualization of comparative genomics.

Copyright Owner

Paul Mangiamele

Language

en

File Format

application/pdf

File Size

81 pages

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