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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2017
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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. |
format | Online Article Text |
id | pubmed-5610716 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
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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