July 7, 2019  |  

A hybrid approach for the automated finishing of bacterial genomes.

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

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.

Journal: Nature biotechnology
DOI: 10.1038/nbt.2288
Year: 2012

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