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High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

Nature Reviews Microbiology volume 10, pages 599–606 (2012)Cite this article

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Abstract

Here, we take a snapshot of the high-throughput sequencing platforms, together with the relevant analytical tools, that are available to microbiologists in 2012, and evaluate the strengths and weaknesses of these platforms in obtaining bacterial genome sequences. We also scan the horizon of future possibilities, speculating on how the availability of sequencing that is 'too cheap to metre' might change the face of microbiology forever.

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Figure 1: High-throughput sequencing platforms.

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Acknowledgements

The authors thank the anonymous reviewers for their help and suggestions.

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Authors and Affiliations

  1. Nicholas J. Loman, Chrystala Constantinidou, Jacqueline Z. M. Chan, Mihail Halachev, Martin Sergeant, Charles W. Penn and Mark J. Pallen are at the Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.,

    Nicholas J. Loman, Chrystala Constantinidou, Jacqueline Z. M. Chan, Mihail Halachev, Martin Sergeant, Charles W. Penn & Mark J. Pallen

  2. Esther R. Robinson is at the Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, UK.,

    Esther R. Robinson

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  1. Nicholas J. Loman
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Correspondence to Mark J. Pallen.

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Competing interests

Mark J. Pallen was a winner of an Ion Personal Genome Machine (PGM) (from Ion Torrent, part of Life Technologies) in the European Ion PGM Grant Programme. Nicholas J. Loman has received expenses to speak at an Ion Torrent meeting organized by Life Technologies and has received honoraria and expenses from Illumina to speak at Illumina meetings. Chrystala Constantinidou, Jacqueline Z. M. Chan, Mihail Halachev, Martin Sergeant, Charles W. Penn and Esther R. Robinson declare no competing financial interests.

Supplementary information

Supplementary information S1 (table)

Available read mapping and de novo assembly software for next-generation sequence data (PDF 275 kb)

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Loman, N., Constantinidou, C., Chan, J. et al. High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 10, 599–606 (2012). https://doi.org/10.1038/nrmicro2850

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