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CORRESPONDENCE Open Access Correspondence Finishing genomes with limited resources: lessons from an ensemble of microbial genomes

By Niranjan Nagarajan, Christopher Cook, Mariapia Di Bonaventura, Hong Ge, Allen Richards, Kimberly A Bishop, Robert Desalle, Timothy D Read and Mihai Pop

Abstract

While 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. Background Not long ago, the expected outcome of a microbial genome project was the complete DNA sequence of all the chromosomes and extra-chromosomal elements o

Year: 2013
OAI identifier: oai:CiteSeerX.psu:10.1.1.352.6157
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