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Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types

The study of the microbiome data holds great potential for elucidating the biological and metabolic functioning of living organisms and their role in the environment. Metagenomic analyses have shown that humans, along with for example, domestic animals, wildlife and arthropods, are colonized by an i...

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Autores principales: Plyusnin, Ilya, Kant, Ravi, Jääskeläinen, Anne J, Sironen, Tarja, Holm, Liisa, Vapalahti, Olli, Smura, Teemu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7772471/
https://www.ncbi.nlm.nih.gov/pubmed/33408878
http://dx.doi.org/10.1093/ve/veaa091
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author Plyusnin, Ilya
Kant, Ravi
Jääskeläinen, Anne J
Sironen, Tarja
Holm, Liisa
Vapalahti, Olli
Smura, Teemu
author_facet Plyusnin, Ilya
Kant, Ravi
Jääskeläinen, Anne J
Sironen, Tarja
Holm, Liisa
Vapalahti, Olli
Smura, Teemu
author_sort Plyusnin, Ilya
collection PubMed
description The study of the microbiome data holds great potential for elucidating the biological and metabolic functioning of living organisms and their role in the environment. Metagenomic analyses have shown that humans, along with for example, domestic animals, wildlife and arthropods, are colonized by an immense community of viruses. The current Coronavirus pandemic (COVID-19) heightens the need to rapidly detect previously unknown viruses in an unbiased way. The increasing availability of metagenomic data in this era of next-generation sequencing (NGS), along with increasingly affordable sequencing technologies, highlight the need for reliable and comprehensive methods to manage such data. In this article, we present a novel bioinformatics pipeline called LAZYPIPE for identifying both previously known and novel viruses in host associated or environmental samples and give examples of virus discovery based on it. LAZYPIPE is a Unix-based pipeline for automated assembling and taxonomic profiling of NGS libraries implemented as a collection of C++, Perl, and R scripts.
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spelling pubmed-77724712021-01-05 Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Plyusnin, Ilya Kant, Ravi Jääskeläinen, Anne J Sironen, Tarja Holm, Liisa Vapalahti, Olli Smura, Teemu Virus Evol Resources The study of the microbiome data holds great potential for elucidating the biological and metabolic functioning of living organisms and their role in the environment. Metagenomic analyses have shown that humans, along with for example, domestic animals, wildlife and arthropods, are colonized by an immense community of viruses. The current Coronavirus pandemic (COVID-19) heightens the need to rapidly detect previously unknown viruses in an unbiased way. The increasing availability of metagenomic data in this era of next-generation sequencing (NGS), along with increasingly affordable sequencing technologies, highlight the need for reliable and comprehensive methods to manage such data. In this article, we present a novel bioinformatics pipeline called LAZYPIPE for identifying both previously known and novel viruses in host associated or environmental samples and give examples of virus discovery based on it. LAZYPIPE is a Unix-based pipeline for automated assembling and taxonomic profiling of NGS libraries implemented as a collection of C++, Perl, and R scripts. Oxford University Press 2020-12-02 /pmc/articles/PMC7772471/ /pubmed/33408878 http://dx.doi.org/10.1093/ve/veaa091 Text en © The Author(s) 2020. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Resources
Plyusnin, Ilya
Kant, Ravi
Jääskeläinen, Anne J
Sironen, Tarja
Holm, Liisa
Vapalahti, Olli
Smura, Teemu
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types
title Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types
title_full Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types
title_fullStr Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types
title_full_unstemmed Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types
title_short Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types
title_sort novel ngs pipeline for virus discovery from a wide spectrum of hosts and sample types
topic Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7772471/
https://www.ncbi.nlm.nih.gov/pubmed/33408878
http://dx.doi.org/10.1093/ve/veaa091
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