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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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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). |
format | Online Article Text |
id | pubmed-9673492 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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