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What the Phage: a scalable workflow for the identification and analysis of phage sequences

Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approa...

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Autores principales: Marquet, Mike, Hölzer, Martin, Pletz, Mathias W, Viehweger, Adrian, Makarewicz, Oliwia, Ehricht, Ralf, Brandt, Christian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9673492/
https://www.ncbi.nlm.nih.gov/pubmed/36399058
http://dx.doi.org/10.1093/gigascience/giac110
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author Marquet, Mike
Hölzer, Martin
Pletz, Mathias W
Viehweger, Adrian
Makarewicz, Oliwia
Ehricht, Ralf
Brandt, Christian
author_facet Marquet, Mike
Hölzer, Martin
Pletz, Mathias W
Viehweger, Adrian
Makarewicz, Oliwia
Ehricht, Ralf
Brandt, Christian
author_sort Marquet, Mike
collection PubMed
description Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, developed “What the Phage” (WtP), an easy-to-use and parallel multitool approach for phage prediction combined with an annotation and classification downstream strategy, thus supporting the user's decision-making process by summarizing the results of the different prediction tools in charts and tables. WtP is reproducible and scales to thousands of datasets through a workflow manager (Nextflow). WtP is freely available under a GPL-3.0 license (https://github.com/replikation/What_the_Phage).
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spelling pubmed-96734922022-11-21 What the Phage: a scalable workflow for the identification and analysis of phage sequences Marquet, Mike Hölzer, Martin Pletz, Mathias W Viehweger, Adrian Makarewicz, Oliwia Ehricht, Ralf Brandt, Christian Gigascience Technical Note Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, developed “What the Phage” (WtP), an easy-to-use and parallel multitool approach for phage prediction combined with an annotation and classification downstream strategy, thus supporting the user's decision-making process by summarizing the results of the different prediction tools in charts and tables. WtP is reproducible and scales to thousands of datasets through a workflow manager (Nextflow). WtP is freely available under a GPL-3.0 license (https://github.com/replikation/What_the_Phage). Oxford University Press 2022-11-18 /pmc/articles/PMC9673492/ /pubmed/36399058 http://dx.doi.org/10.1093/gigascience/giac110 Text en © The Author(s) 2022. Published by Oxford University Press GigaScience. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Note
Marquet, Mike
Hölzer, Martin
Pletz, Mathias W
Viehweger, Adrian
Makarewicz, Oliwia
Ehricht, Ralf
Brandt, Christian
What the Phage: a scalable workflow for the identification and analysis of phage sequences
title What the Phage: a scalable workflow for the identification and analysis of phage sequences
title_full What the Phage: a scalable workflow for the identification and analysis of phage sequences
title_fullStr What the Phage: a scalable workflow for the identification and analysis of phage sequences
title_full_unstemmed What the Phage: a scalable workflow for the identification and analysis of phage sequences
title_short What the Phage: a scalable workflow for the identification and analysis of phage sequences
title_sort what the phage: a scalable workflow for the identification and analysis of phage sequences
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9673492/
https://www.ncbi.nlm.nih.gov/pubmed/36399058
http://dx.doi.org/10.1093/gigascience/giac110
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