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Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks

Nature Biotechnology volume 31, pages 592–594 (2013)Cite this article

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In their paper “Performance comparison of benchtop high-throughput sequencing platforms” published in the May 2012 issue, Loman et al.1 provide a detailed comparison of the metrics associated with three different benchtop DNA sequencing platforms for the assembly of a single genome. Information was given on read-level metrics, such as length, accuracy and alignment, and on assembly-level metrics, such as contig N50 and gap number. The results were discussed in the context of the utility of whole-genome sequencing for public health microbiology.

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Authors and Affiliations

  1. Wellcome Trust Sanger Institute, Hinxton, UK

    Simon R Harris, Michael A Quail, Sharon J Peacock & Julian Parkhill

  2. University of Cambridge, Cambridge, UK

    M E Török, Edward J P Cartwright & Sharon J Peacock

  3. Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK

    M E Török, Edward J P Cartwright & Sharon J Peacock

  4. Public Health England, Cambridge, UK

    M E Török, Edward J P Cartwright & Sharon J Peacock

Authors
  1. Simon R Harris
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  2. M E Török
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  3. Edward J P Cartwright
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  4. Michael A Quail
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  5. Sharon J Peacock
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  6. Julian Parkhill
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Correspondence to Julian Parkhill.

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Competing interests

J.P. has received funding for conference travel and accommodations from Pacific Biosciences and Illumina. S.J.P. is a consultant for Pfizer.

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Harris, S., Török, M., Cartwright, E. et al. Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks. Nat Biotechnol 31, 592–594 (2013). https://doi.org/10.1038/nbt.2616

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