A hybrid approach for the automated finishing of bacterial genomes

Ali Bashir; Aaron A. Klammer; William P. Robins; Chen Shan Chin; Dale Webster; Ellen Paxinos; David Hsu; Meredith Ashby; Susana Wang; Paul Peluso; Robert Sebra; Jon Sorenson; James Bullard; Jackie Yen; Marie Valdovino; Emilia Mollova; Khai Luong; Steven Lin; Brianna Lamay; Amruta Joshi; Lori Rowe; Michael Frace; Cheryl L. Tarr; Maryann Turnsek; Brigid M. Davis; Andrew Kasarskis; John J. Mekalanos; Matthew K. Waldor; Eric E. Schadt

doi:10.1038/nbt.2288

A hybrid approach for the automated finishing of bacterial genomes

Ali Bashir, Aaron A. Klammer, William P. Robins, Chen Shan Chin, Dale Webster, Ellen Paxinos, David Hsu, Meredith Ashby, Susana Wang, Paul Peluso, Robert Sebra, Jon Sorenson, James Bullard, Jackie Yen, Marie Valdovino, Emilia Mollova, Khai Luong, Steven Lin, Brianna Lamay, Amruta JoshiLori Rowe, Michael Frace, Cheryl L. Tarr, Maryann Turnsek, Brigid M. Davis, Andrew Kasarskis, John J. Mekalanos, Matthew K. Waldor, Eric E. Schadt

Research output: Contribution to journal › Article › peer-review

149 Scopus citations

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.

Original language	English
Pages (from-to)	701-707
Number of pages	7
Journal	Nature Biotechnology
Volume	30
Issue number	7
DOIs	https://doi.org/10.1038/nbt.2288
State	Published - Jul 2012

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Bashir, A., Klammer, A. A., Robins, W. P., Chin, C. S., Webster, D., Paxinos, E., Hsu, D., Ashby, M., Wang, S., Peluso, P., Sebra, R., Sorenson, J., Bullard, J., Yen, J., Valdovino, M., Mollova, E., Luong, K., Lin, S., Lamay, B., ... Schadt, E. E. (2012). A hybrid approach for the automated finishing of bacterial genomes. Nature Biotechnology, 30(7), 701-707. https://doi.org/10.1038/nbt.2288

@article{ebb955de77a248c3afff96bc04115499,

title = "A hybrid approach for the automated finishing of bacterial genomes",

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.",

author = "Ali Bashir and Klammer, {Aaron A.} and Robins, {William P.} and Chin, {Chen Shan} and Dale Webster and Ellen Paxinos and David Hsu and Meredith Ashby and Susana Wang and Paul Peluso and Robert Sebra and Jon Sorenson and James Bullard and Jackie Yen and Marie Valdovino and Emilia Mollova and Khai Luong and Steven Lin and Brianna Lamay and Amruta Joshi and Lori Rowe and Michael Frace and Tarr, {Cheryl L.} and Maryann Turnsek and Davis, {Brigid M.} and Andrew Kasarskis and Mekalanos, {John J.} and Waldor, {Matthew K.} and Schadt, {Eric E.}",

note = "Funding Information: 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.).",

year = "2012",

month = jul,

doi = "10.1038/nbt.2288",

language = "English",

volume = "30",

pages = "701--707",

journal = "Nature Biotechnology",

issn = "1087-0156",

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Bashir, A, Klammer, AA, Robins, WP, Chin, CS, Webster, D, Paxinos, E, Hsu, D, Ashby, M, Wang, S, Peluso, P, Sebra, R, Sorenson, J, Bullard, J, Yen, J, Valdovino, M, Mollova, E, Luong, K, Lin, S, Lamay, B, Joshi, A, Rowe, L, Frace, M, Tarr, CL, Turnsek, M, Davis, BM, Kasarskis, A, Mekalanos, JJ, Waldor, MK & Schadt, EE 2012, 'A hybrid approach for the automated finishing of bacterial genomes', Nature Biotechnology, vol. 30, no. 7, pp. 701-707. https://doi.org/10.1038/nbt.2288

TY - JOUR

T1 - A hybrid approach for the automated finishing of bacterial genomes

AU - Bashir, Ali

AU - Klammer, Aaron A.

AU - Robins, William P.

AU - Chin, Chen Shan

AU - Webster, Dale

AU - Paxinos, Ellen

AU - Hsu, David

AU - Ashby, Meredith

AU - Wang, Susana

AU - Peluso, Paul

AU - Sebra, Robert

AU - Sorenson, Jon

AU - Bullard, James

AU - Yen, Jackie

AU - Valdovino, Marie

AU - Mollova, Emilia

AU - Luong, Khai

AU - Lin, Steven

AU - Lamay, Brianna

AU - Joshi, Amruta

AU - Rowe, Lori

AU - Frace, Michael

AU - Tarr, Cheryl L.

AU - Turnsek, Maryann

AU - Davis, Brigid M.

AU - Kasarskis, Andrew

AU - Mekalanos, John J.

AU - Waldor, Matthew K.

AU - Schadt, Eric E.

N1 - Funding Information: 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.).

PY - 2012/7

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N2 - 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.

AB - 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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U2 - 10.1038/nbt.2288

DO - 10.1038/nbt.2288

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VL - 30

SP - 701

EP - 707

JO - Nature Biotechnology

JF - Nature Biotechnology

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ER -

A hybrid approach for the automated finishing of bacterial genomes

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