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    Comparison of classical multi-locus sequence typing software for next-generation sequencing data

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    Author
    Page, AJ; Alikhan, N-F; Carleton, HA; Seemann, T; Keane, JA; Katz, LS
    Date
    2017-08-01
    Source Title
    Microbial Genomics
    Publisher
    MICROBIOLOGY SOC
    University of Melbourne Author/s
    Seemann, Torsten
    Affiliation
    Microbiology and Immunology
    Metadata
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    Document Type
    Journal Article
    Citations
    Page, A. J., Alikhan, N. -F., Carleton, H. A., Seemann, T., Keane, J. A. & Katz, L. S. (2017). Comparison of classical multi-locus sequence typing software for next-generation sequencing data. MICROBIAL GENOMICS, 3 (8), https://doi.org/10.1099/mgen.0.000124.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/257255
    DOI
    10.1099/mgen.0.000124
    Abstract
    Multi-locus sequence typing (MLST) is a widely used method for categorizing bacteria. Increasingly, MLST is being performed using next-generation sequencing (NGS) data by reference laboratories and for clinical diagnostics. Many software applications have been developed to calculate sequence types from NGS data; however, there has been no comprehensive review to date on these methods. We have compared eight of these applications against real and simulated data, and present results on: (1) the accuracy of each method against traditional typing methods, (2) the performance on real outbreak datasets, (3) the impact of contamination and varying depth of coverage, and (4) the computational resource requirements.

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