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

ABSTRACT: 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).

SUBMITTER: Marquet M

PROVIDER: S-EPMC9673492 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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

Marquet Mike M Hölzer Martin M Pletz Mathias W MW Viehweger Adrian A Makarewicz Oliwia O Ehricht Ralf R Brandt Christian C

GigaScience 20221101

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 downst ...[more]

PMID: 36399058

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