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Comparison of classical multi-locus sequence typing software for next-generation sequencing data
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Page, Andrew J., Alikhan, Nabil-Fareed, Carleton, Heather A., Seemann, Torsten, Keane, Jacqueline A. and Katz, Lee S. (2017) Comparison of classical multi-locus sequence typing software for next-generation sequencing data. Microbial Genomics, 3 (8). e000124. doi:10.1099/mgen.0.000124 ISSN 2057-5858.
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Official URL: http://dx.doi.org/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.
Item Type: | Journal Article | |||||||||
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Subjects: | Q Science > QR Microbiology | |||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection | |||||||||
Library of Congress Subject Headings (LCSH): | Bacteria -- Classification -- Software, Bacteria -- Phylogeny, Bacteria -- Genetic aspects | |||||||||
Journal or Publication Title: | Microbial Genomics | |||||||||
Publisher: | Microbiology Society | |||||||||
ISSN: | 2057-5858 | |||||||||
Official Date: | 31 August 2017 | |||||||||
Dates: |
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Volume: | 3 | |||||||||
Number: | 8 | |||||||||
Article Number: | e000124 | |||||||||
DOI: | 10.1099/mgen.0.000124 | |||||||||
Status: | Peer Reviewed | |||||||||
Publication Status: | Published | |||||||||
Access rights to Published version: | Open Access (Creative Commons) | |||||||||
Date of first compliant deposit: | 6 December 2017 | |||||||||
Date of first compliant Open Access: | 7 December 2017 | |||||||||
RIOXX Funder/Project Grant: |
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