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

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 f...

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Detalles Bibliográficos
Autores principales: Page, Andrew J., Alikhan, Nabil-Fareed, Carleton, Heather A., Seemann, Torsten, Keane, Jacqueline A., Katz, Lee S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5610716/
https://www.ncbi.nlm.nih.gov/pubmed/29026660
http://dx.doi.org/10.1099/mgen.0.000124
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author Page, Andrew J.
Alikhan, Nabil-Fareed
Carleton, Heather A.
Seemann, Torsten
Keane, Jacqueline A.
Katz, Lee S.
author_facet Page, Andrew J.
Alikhan, Nabil-Fareed
Carleton, Heather A.
Seemann, Torsten
Keane, Jacqueline A.
Katz, Lee S.
author_sort Page, Andrew J.
collection PubMed
description 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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spelling pubmed-56107162017-10-12 Comparison of classical multi-locus sequence typing software for next-generation sequencing data Page, Andrew J. Alikhan, Nabil-Fareed Carleton, Heather A. Seemann, Torsten Keane, Jacqueline A. Katz, Lee S. Microb Genom Review 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. Microbiology Society 2017-07-04 /pmc/articles/PMC5610716/ /pubmed/29026660 http://dx.doi.org/10.1099/mgen.0.000124 Text en © 2017 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.
spellingShingle Review
Page, Andrew J.
Alikhan, Nabil-Fareed
Carleton, Heather A.
Seemann, Torsten
Keane, Jacqueline A.
Katz, Lee S.
Comparison of classical multi-locus sequence typing software for next-generation sequencing data
title Comparison of classical multi-locus sequence typing software for next-generation sequencing data
title_full Comparison of classical multi-locus sequence typing software for next-generation sequencing data
title_fullStr Comparison of classical multi-locus sequence typing software for next-generation sequencing data
title_full_unstemmed Comparison of classical multi-locus sequence typing software for next-generation sequencing data
title_short Comparison of classical multi-locus sequence typing software for next-generation sequencing data
title_sort comparison of classical multi-locus sequence typing software for next-generation sequencing data
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5610716/
https://www.ncbi.nlm.nih.gov/pubmed/29026660
http://dx.doi.org/10.1099/mgen.0.000124
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