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ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis
Bacteriophages play central roles in the maintenance and function of most ecosystems by regulating bacterial communities. Yet, our understanding of their diversity remains limited due to the lack of robust bioinformatics standards. Here we present ViroProfiler, an in-silico workflow for analyzing sh...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Taylor & Francis
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10072060/ https://www.ncbi.nlm.nih.gov/pubmed/36998174 http://dx.doi.org/10.1080/19490976.2023.2192522 |
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author | Ru, Jinlong Khan Mirzaei, Mohammadali Xue, Jinling Peng, Xue Deng, Li |
author_facet | Ru, Jinlong Khan Mirzaei, Mohammadali Xue, Jinling Peng, Xue Deng, Li |
author_sort | Ru, Jinlong |
collection | PubMed |
description | Bacteriophages play central roles in the maintenance and function of most ecosystems by regulating bacterial communities. Yet, our understanding of their diversity remains limited due to the lack of robust bioinformatics standards. Here we present ViroProfiler, an in-silico workflow for analyzing shotgun viral metagenomic data. ViroProfiler can be executed on a local Linux computer or cloud computing environments. It uses the containerization technique to ensure computational reproducibility and facilitate collaborative research. ViroProfiler is freely available at https://github.com/deng-lab/viroprofiler. |
format | Online Article Text |
id | pubmed-10072060 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Taylor & Francis |
record_format | MEDLINE/PubMed |
spelling | pubmed-100720602023-04-05 ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis Ru, Jinlong Khan Mirzaei, Mohammadali Xue, Jinling Peng, Xue Deng, Li Gut Microbes Brief Report Bacteriophages play central roles in the maintenance and function of most ecosystems by regulating bacterial communities. Yet, our understanding of their diversity remains limited due to the lack of robust bioinformatics standards. Here we present ViroProfiler, an in-silico workflow for analyzing shotgun viral metagenomic data. ViroProfiler can be executed on a local Linux computer or cloud computing environments. It uses the containerization technique to ensure computational reproducibility and facilitate collaborative research. ViroProfiler is freely available at https://github.com/deng-lab/viroprofiler. Taylor & Francis 2023-03-30 /pmc/articles/PMC10072060/ /pubmed/36998174 http://dx.doi.org/10.1080/19490976.2023.2192522 Text en © 2023 The Author(s). Published with license by Taylor & Francis Group, LLC. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent. |
spellingShingle | Brief Report Ru, Jinlong Khan Mirzaei, Mohammadali Xue, Jinling Peng, Xue Deng, Li ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis |
title | ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis |
title_full | ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis |
title_fullStr | ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis |
title_full_unstemmed | ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis |
title_short | ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis |
title_sort | viroprofiler: a containerized bioinformatics pipeline for viral metagenomic data analysis |
topic | Brief Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10072060/ https://www.ncbi.nlm.nih.gov/pubmed/36998174 http://dx.doi.org/10.1080/19490976.2023.2192522 |
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