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A hybrid approach for the automated finishing of bacterial genomes


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.

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Figure 1: H1 assembly.
Figure 2: Resolution of rRNA genes.
Figure 3: CTX-TLC assembly and validation.
Figure 4: Superintegron assembly.

Accession codes

Primary accessions


NCBI Reference Sequence

Sequence Read Archive

Referenced accessions

NCBI Reference Sequence


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This study was supported in part by the US National Institutes of Health National Institute of General Medical Sciences grant R01GM068851 (J.J.M. and W.P.R.), NIH R37 AI-42347 (B.M.D. and M.K.W.) and the Howard Hughes Medical Institute (B.M.D. and M.K.W.).

Author information




A.B., A.A.K., W.P.R., C.S.C., E.P., M.F., C.L.T., M.T., B.M.D., A.K., J.J.M., M.K.W. and E.E.S. designed the experiments; A.B., A.A.K., C.S.C., D.W., J.S. and J.B. designed the methods; W.P.R., E.P., D.H., M.A., S.W., P.P., R.S., J.Y., M.V., E.M., K.L., S.L., B.L., A.J., L.R., M.F., C.L.T., M.T. and B.M.D. carried out all sample-preparation experiments, all sequencing runs and PCR-validation experiments; A.B., A.A.K., W.P.R., C.S.C., D.W., J.B., A.A.K., M.K.W. and E.E.S. jointly analyzed the data sets; and A.B., A.A.K., W.P.R., L.R., M.F., C.L.T., M.T., B.M.D., J.J.M., M.K.W. and E.E.S. wrote the manuscript.

Corresponding author

Correspondence to Eric E Schadt.

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Many of the authors are employees of and own stock in Pacific Biosciences.

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Supplementary Methods, Supplementary Results, Supplementary Tables 1-9 and Supplementary Figs. 1-13 (PDF 2063 kb)

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Bashir, A., Klammer, A., Robins, W. et al. A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol 30, 701–707 (2012).

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