Solving the problem of comparing whole bacterial genomes across different sequencing platforms.

Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one te...

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Autores principales:	Rolf S Kaas, Pimlapas Leekitcharoenphon, Frank M Aarestrup, Ole Lund
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6b14e92c3f19443f9b4c71db152fc9ec
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spelling	oai:doaj.org-article:6b14e92c3f19443f9b4c71db152fc9ec2021-11-25T06:05:24ZSolving the problem of comparing whole bacterial genomes across different sequencing platforms.1932-620310.1371/journal.pone.0104984https://doaj.org/article/6b14e92c3f19443f9b4c71db152fc9ec2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25110940/?tool=EBIhttps://doaj.org/toc/1932-6203Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools.Rolf S KaasPimlapas LeekitcharoenphonFrank M AarestrupOle LundPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 8, p e104984 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rolf S Kaas Pimlapas Leekitcharoenphon Frank M Aarestrup Ole Lund Solving the problem of comparing whole bacterial genomes across different sequencing platforms.
description	Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools.
format	article
author	Rolf S Kaas Pimlapas Leekitcharoenphon Frank M Aarestrup Ole Lund
author_facet	Rolf S Kaas Pimlapas Leekitcharoenphon Frank M Aarestrup Ole Lund
author_sort	Rolf S Kaas
title	Solving the problem of comparing whole bacterial genomes across different sequencing platforms.
title_short	Solving the problem of comparing whole bacterial genomes across different sequencing platforms.
title_full	Solving the problem of comparing whole bacterial genomes across different sequencing platforms.
title_fullStr	Solving the problem of comparing whole bacterial genomes across different sequencing platforms.
title_full_unstemmed	Solving the problem of comparing whole bacterial genomes across different sequencing platforms.
title_sort	solving the problem of comparing whole bacterial genomes across different sequencing platforms.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/6b14e92c3f19443f9b4c71db152fc9ec
work_keys_str_mv	AT rolfskaas solvingtheproblemofcomparingwholebacterialgenomesacrossdifferentsequencingplatforms AT pimlapasleekitcharoenphon solvingtheproblemofcomparingwholebacterialgenomesacrossdifferentsequencingplatforms AT frankmaarestrup solvingtheproblemofcomparingwholebacterialgenomesacrossdifferentsequencingplatforms AT olelund solvingtheproblemofcomparingwholebacterialgenomesacrossdifferentsequencingplatforms
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Solving the problem of comparing whole bacterial genomes across different sequencing platforms.

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