Scaling short read de novo DNA sequence assembly to gigabase genomes

Cook, Jeffrey J.

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https://hdl.handle.net/2142/24291 Copy

Description

Title

Scaling short read de novo DNA sequence assembly to gigabase genomes

Author(s)

Cook, Jeffrey J.

Issue Date

2011-05-25T15:03:13Z

Director of Research (if dissertation) or Advisor (if thesis)

Zilles, Craig

Doctoral Committee Chair(s)

Zilles, Craig

Committee Member(s)

• Hudson, Matthew E.
• Lumetta, Steven S.
• Patel, Sanjay J.
• Wong, Martin D.F.

Department of Study

Electrical & Computer Eng

Discipline

Electrical & Computer Engr

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Date of Ingest

2011-05-25T15:03:13Z

Keyword(s)

• de novo sequence assembly
• de Bruijn graph
• Eulerian assembly
• gigabase genome assembly
• Deoxyribonucleic Acid (DNA)
• short reads
• massively parallel sequencing

Abstract

The recent advent of massively parallel sequencing technologies has drastically reduced the cost of sequencing, sparking a revolution in whole genome de novo sequencing. However, these new technologies sample much shorter segments of DNA, called short reads, than conventional but more costly long read sequencing technologies, and suffer from higher and more varied error rates. Modern genome assembly tools compensate for these shortcomings by using de Bruijn graph based assembly techniques; however, for large genomes, the physical memory required to efficiently build and manipulate the de Bruijn graph generally far exceeds that which is available on modern commodity workstations. This dissertation develops novel out-of-core algorithms that permit conservative assembly of the de Bruijn graph using one to three orders of magnitude less memory than is required by the naïve approach. These algorithms are implemented in an open source genome assembly tool that replaces the front-end assembly process, which can connect to existing back-end tools in a manner that attempts to decouple the phases that have performance concerns but simple heuristics, from those that have complex heuristics but relatively straightforward implementations, in a way that allows each to be developed by domain experts.

Graduation Semester

2011-05

Permalink

http://hdl.handle.net/2142/24291

Copyright and License Information

Copyright 2011 Jeffrey J. Cook

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