PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data

Abstract The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cyc...

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Autores principales:	Julian R. Garneau, Florence Depardieu, Louis-Charles Fortier, David Bikard, Marc Monot
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f7de9c00525a49ff9dc9d8b9e894e1b8
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spelling	oai:doaj.org-article:f7de9c00525a49ff9dc9d8b9e894e1b82021-12-02T12:30:26ZPhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data10.1038/s41598-017-07910-52045-2322https://doaj.org/article/f7de9c00525a49ff9dc9d8b9e894e1b82017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-07910-5https://doaj.org/toc/2045-2322Abstract The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cycle, phage-host interactions, and evolution. In this work, we demonstrate how it is possible to recover more information from sequencing data than just the phage genome. We developed a theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data. Our method relies on the detection of biases in the number of reads, which are observable at natural DNA termini compared with the rest of the phage genome. We implemented our method with the creation of the software PhageTerm and validated it using a set of phages with well-established packaging mechanisms representative of the termini diversity, i.e. 5′cos (Lambda), 3′cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, we determined the termini of nine Clostridium difficile phages and six phages whose sequences were retrieved from the Sequence Read Archive. PhageTerm is freely available (https://sourceforge.net/projects/phageterm), as a Galaxy ToolShed and on a Galaxy-based server (https://galaxy.pasteur.fr).Julian R. GarneauFlorence DepardieuLouis-Charles FortierDavid BikardMarc MonotNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Julian R. Garneau Florence Depardieu Louis-Charles Fortier David Bikard Marc Monot PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data
description	Abstract The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cycle, phage-host interactions, and evolution. In this work, we demonstrate how it is possible to recover more information from sequencing data than just the phage genome. We developed a theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data. Our method relies on the detection of biases in the number of reads, which are observable at natural DNA termini compared with the rest of the phage genome. We implemented our method with the creation of the software PhageTerm and validated it using a set of phages with well-established packaging mechanisms representative of the termini diversity, i.e. 5′cos (Lambda), 3′cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, we determined the termini of nine Clostridium difficile phages and six phages whose sequences were retrieved from the Sequence Read Archive. PhageTerm is freely available (https://sourceforge.net/projects/phageterm), as a Galaxy ToolShed and on a Galaxy-based server (https://galaxy.pasteur.fr).
format	article
author	Julian R. Garneau Florence Depardieu Louis-Charles Fortier David Bikard Marc Monot
author_facet	Julian R. Garneau Florence Depardieu Louis-Charles Fortier David Bikard Marc Monot
author_sort	Julian R. Garneau
title	PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data
title_short	PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data
title_full	PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data
title_fullStr	PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data
title_full_unstemmed	PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data
title_sort	phageterm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/f7de9c00525a49ff9dc9d8b9e894e1b8
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PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data

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