Finishing genomes with limited resources: lessons from an ensemble of microbial genomes

dc.contributor.authorNagarajan, Niranjan
dc.contributor.authorCook, Christopher
dc.contributor.authorDi Bonaventura, MariaPia
dc.contributor.authorGe, Hong
dc.contributor.authorRichards, Allen
dc.contributor.authorBishop-Lilly, Kimberly A
dc.contributor.authorDeSalle, Robert
dc.contributor.authorRead, Timothy D
dc.contributor.authorPop, Mihai
dc.date.accessioned2013-01-10T21:27:21Z
dc.date.available2013-01-10T21:27:21Z
dc.date.issued2010-04-16
dc.description.abstractWhile new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for highpriority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.en_US
dc.description.urihttps://doi.org/10.1186/1471-2164-11-242
dc.identifier.citationNagarajan, N., Cook, C., Di Bonaventura, M. et al. Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC Genomics 11, 242 (2010).en_US
dc.identifier.urihttp://hdl.handle.net/1903/13372
dc.language.isoen_USen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Natural Sciencesen_us
dc.relation.isAvailableAtComputer Scienceen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectmicrobial genomesen_US
dc.titleFinishing genomes with limited resources: lessons from an ensemble of microbial genomesen_US
dc.typeArticleen_US

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