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Nat Biotechnol. 2012 Jul 1;30(7):701-707. doi: 10.1038/nbt.2288.

A hybrid approach for the automated finishing of bacterial genomes.

Author information

1
Pacific Biosciences, Menlo Park, CA.
2
Department of Medicine, Harvard Medical School, Boston, MA.
3
National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta GA 30333.
4
Channing Laboratory, Brigham and Women's Hospital, Boston, MA.
5
Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA.
6
Howard Hughes Medical Institute, Boston, MA.
7
Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York City.
#
Contributed equally

Abstract

Advances in DNA sequencing technology have improved our ability to characterize most genomic diversity. However, accurate resolution of large structural events is challenging because of the short read lengths of second-generation technologies. Third-generation sequencing technologies, which can yield longer multikilobase reads, have the potential to address limitations associated with genome assembly. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at >99.9% accuracy. Complex regions with clinically relevant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 cholera reference strain, we obtained 14 scaffolds of greater than 1 kb for the experimental data and 8 scaffolds of greater than 1 kb for the simulated data, which allowed us to correct several errors in contigs assembled from the short-read data alone. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly.

PMID:
22750883
PMCID:
PMC3731737
DOI:
10.1038/nbt.2288
[Indexed for MEDLINE]
Free PMC Article

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