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

• Type of Material: Article
• Authors: Niranjan Nagarajan, Genome Institute of Singapore; Christopher Cook, Naval Medical Research Center; MariaPia Di Bonaventura, American Museum of Natural History; Hong Ge, Naval Medical Research Center; Allen Richards, Naval Medical Research Center; Kimberly A. Bishop-Lilly, Naval Medical Research Center; Robert DeSalle, American Museum of Natural History; Timothy D Read, Emory University; Mihai Pop, University of Maryland
• Language: English
• Date: 2010
• Publisher: BioMed Central
• Publication Version: Final Published Version
• Copyright Statement: ©2010 The Article is a work of the United States Government; licensee BioMed Central Ltd.
• License: Creative Commons Attribution 2.0 Generic
• Final Published Version (URL): http://www.biomedcentral.com/1471-2164/11/242
• Title of Journal or Parent Work: BMC Genomics
• ISSN: 1471-2164
• Volume: 11
• Issue: 242
• Grant/Funding Information: The views expressed in this article are those of the authors and do not necessarily reflect the official policy or position of the Department of the Navy, Department of Defense, nor the U.S. Government.; The authors are supported in part by Department of Defense Transformational Medical Technologies initiative TMTI0068 07 NM T to T.D.R. and NSF grant IIS-0812111 (to M.P.).
• Research Categories: Biology, Microbiology; Biology, Genetics

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 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.