Assembly complexity of prokaryotic genomes using short reads

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dc.contributor.authorKingsford, Carl
dc.contributor.authorSchatz, Michael C
dc.contributor.authorPop, Mihai
dc.date.accessioned2013-01-10T21:33:50Z
dc.date.available2013-01-10T21:33:50Z
dc.date.issued2010-01-12
dc.description.abstractBackground: 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.en_US
dc.description.urihttps://doi.org/10.1186/1471-2105-11-21
dc.identifier.citationKingsford, C., Schatz, M.C. & Pop, M. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11, 21 (2010).en_US
dc.identifier.urihttp://hdl.handle.net/1903/13377
dc.language.isoen_USen_US
dc.relation.isAvailableAtA. James Clark School of Engineeringen_us
dc.relation.isAvailableAtFischell Department of Bioengineeringen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectprokaryotic genomesen_US
dc.subjectde Bruijn graphsen_US
dc.titleAssembly complexity of prokaryotic genomes using short readsen_US
dc.typeArticleen_US

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