Open Access Highly Accessed Correspondence

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

Niranjan Nagarajan1*, Christopher Cook34, MariaPia Di Bonaventura5, Hong Ge34, Allen Richards3, Kimberly A Bishop-Lilly34, Robert DeSalle5, Timothy D Read346 and Mihai Pop2

Author affiliations

1 Computational and Mathematical Biology, Genome Institute of Singapore 127726, Singapore

2 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA

3 Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA

4 Henry M. Jackson Foundation, 1401 Rockville Pike, Rockville, MD 20852, USA

5 American Museum of Natural History, New York, NY 10024, USA

6 Division of Infectious Diseases & Department of Human Genetics, Emory University, Atlanta, GA 30322, USA

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Citation and License

BMC Genomics 2010, 11:242  doi:10.1186/1471-2164-11-242

Published: 16 April 2010


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 high-priority 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.