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assembly complexity of prokaryotic genomes using short reads装配使用短读原核基因组的复杂性
Kingsford et al. BMC Bioinformatics 2010, 11:21
/1471-2105/11/21
RESEARCH ARTICLE Open Access
Assembly complexity of prokaryotic genomes
using short reads
*
Carl Kingsford , Michael C Schatz, Mihai Pop
Abstract
Background: De Bruijn graphs are a theoretical framework underlying several modern genome assembly
programs, especially those that deal with very short reads. We describe an application of de Bruijn graphs to
analyze the global repeat structure of prokaryotic genomes.
Results: We provide the first survey of the repeat structure of a large number of genomes. The analysis gives an
upper-bound on the performance of genome assemblers for de novo reconstruction of genomes across a wide
range of read lengths. Further, we demonstrate that the majority of genes in prokaryotic genomes can be
reconstructed uniquely using very short reads even if the genomes themselves cannot. The non-reconstructible
genes are overwhelmingly related to mobile elements (transposons, IS elements, and prophages).
Conclusions: Our results improve upon previous studies on the feasibility of assembly with short reads and
provide a comprehensive benchmark against which to compare the performance of the short-read assemblers
currently being developed.
Background resulting increased redundancy that comes from the
Recently, new technologies developed by 454 Life ability to cheaply sample the same genome many times
Sciences [1], Illumina [2], ABI/SOLiD [3], Helicos [4], over. However, shorter read lengths lead to a much
and others can sequence large quantities of DNA in more computationally challenging assembly problem
only hours. Instead of approximately 1000 nucleotide b
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