ISU Electrical and Computer Engineering Archives

Parallel methods for short read assembly

Jackson, Benjamin G (0016) Parallel methods for short read assembly. PhD thesis, Iowa State University.

Full text available as:

PDF - Requires Adobe Acrobat Reader or other PDF viewer.

Abstract

This work is on the parallel de novo assembly of genomic sequences from short sequence reads. With short reads eliminating the reliability of read overlaps in predicting genomic co-location, a revival of graph-based methods has underpinned the development of short-read assemblers. While these methods predate short read technology, their reach has not extended significantly beyond bacterial genomes due to the memory resources required in their use. These memory limitations are exacerbated by the high coverage needed to compensate for shorter read lengths. As a result, prior to our work, short-read de novo assembly had been demonstrated on relatively small genome sizes with a few million bases. In our work, we advance the field of short sequence assembly in a number of ways. First, we extend models and ideas proposed and tested with small genomes on serial machines to large-scale distributed memory parallel machines. Second, we present ideas for assembly that are especially suited to the reconstruction of very large genomes on these machines. Additionally, we present the first assembler that specifically takes advantage a variable number of fragment sizes or insert lengths concurrently when making assembly decisions, while still working well for data with one insertion length.

EPrint Type:Thesis (PhD)
Uncontrolled Keywords:bioinformatics paired reads transcriptome genome
Subjects:Computer Engineering > SOFTWARE SYSTEMS > Parallel and Distributed Computing
Electrical Engineering > COMMUNICATION & SIGNAL PROCESSING > Bioinformatics
Computer Engineering > SOFTWARE SYSTEMS > Computational Biology and Computational Science
ID Code:503
Identification Number:Identification Number UNSPECIFIED
Deposited By:Benjamin G Jackson
Deposited On:07 July 2009

Archive Staff Only: edit this record