Capstone Title

Progress and Current State of High-Throughput Sequencing Technology

Defense Date

5-2014

Document Type

Capstone

Degree Name

M.S. Biological Sciences

First Advisor

Jose V. Lopez

Second Advisor

Mahmood Shivji

Abstract

The goal of this capstone project will be to look at the current status of the high-throughput sequencing technology. A heavy focus will be placed on the commercial high-throughput sequencing platforms that have come out in the years 2008-2013 which have fallen into two groups: 2nd and 3rd ‘generation’. Nanopore sequencing also known as ‘4th generation’ sequencing will also be discussed as Oxford Nanopore has promised a $900 device that could sequence a 150 million bases in just 6 hours. However, there is no consensus for what constitutes as second, third and fourth generation since technologies continue to change (Ku and Roukos 2013). The goal is to provide a better understanding of which platforms are currently relevant and continue to be so in the near future as a result of costs, quality and applicability.

Improvements in bioinformatics have allowed for the ability to comprehend the increased throughput of data. Thus, an emphasis will be placed on the different types of software, for assembly and mapping, as well as the problems being faced in bioinformatics. A short section will look at the ‘hidden’ costs of sequencing. Case studies, from the past five years, in the fields of whole genome sequencing, transcriptomics, metagenomics, medicine and epigenomics will show the applicability of HTS. Understanding the pros and cons of the different available technologies allows for better utilization of time and money when developing projects.

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