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作者 Cook, Jeffrey J
書名 Scaling short read de novo DNA sequence assembly to gigabase genomes
國際標準書號 9781124964324
book jacket
說明 152 p
附註 Source: Dissertation Abstracts International, Volume: 73-01, Section: B, page: 0023
Adviser: Craig Zilles
Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2011
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 naive 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
School code: 0090
Host Item Dissertation Abstracts International 73-01B
主題 Engineering, Computer
Biology, Bioinformatics
Computer Science
0464
0715
0984
Alt Author University of Illinois at Urbana-Champaign. Electrical & Computer Eng
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