VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing

 : Detection and analysis of viral genomes with Nanopore sequencing has shown great promise in the surveillance of pathogen outbreaks. However, the number of virus detection pipelines supporting Nanopore sequencing is very limited. Here, we present VirPipe, a new pipeline for the detection of viral...

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Autores principales: Kim, Kijin, Park, Kyungmin, Lee, Seonghyeon, Baek, Seung-Hwan, Lim, Tae-Hun, Kim, Jongwoo, Manavalan, Balachandran, Song, Jin-Won, Kim, Won-Keun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10191607/
https://www.ncbi.nlm.nih.gov/pubmed/37129547
http://dx.doi.org/10.1093/bioinformatics/btad293
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author Kim, Kijin
Park, Kyungmin
Lee, Seonghyeon
Baek, Seung-Hwan
Lim, Tae-Hun
Kim, Jongwoo
Manavalan, Balachandran
Song, Jin-Won
Kim, Won-Keun
author_facet Kim, Kijin
Park, Kyungmin
Lee, Seonghyeon
Baek, Seung-Hwan
Lim, Tae-Hun
Kim, Jongwoo
Manavalan, Balachandran
Song, Jin-Won
Kim, Won-Keun
author_sort Kim, Kijin
collection PubMed
description  : Detection and analysis of viral genomes with Nanopore sequencing has shown great promise in the surveillance of pathogen outbreaks. However, the number of virus detection pipelines supporting Nanopore sequencing is very limited. Here, we present VirPipe, a new pipeline for the detection of viral genomes from Nanopore or Illumina sequencing input featuring streamlined installation and customization. AVAILABILITY AND IMPLEMENTATION: VirPipe source code and documentation are freely available for download at https://github.com/KijinKims/VirPipe, implemented in Python and Nextflow.
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spelling pubmed-101916072023-05-18 VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing Kim, Kijin Park, Kyungmin Lee, Seonghyeon Baek, Seung-Hwan Lim, Tae-Hun Kim, Jongwoo Manavalan, Balachandran Song, Jin-Won Kim, Won-Keun Bioinformatics Applications Note  : Detection and analysis of viral genomes with Nanopore sequencing has shown great promise in the surveillance of pathogen outbreaks. However, the number of virus detection pipelines supporting Nanopore sequencing is very limited. Here, we present VirPipe, a new pipeline for the detection of viral genomes from Nanopore or Illumina sequencing input featuring streamlined installation and customization. AVAILABILITY AND IMPLEMENTATION: VirPipe source code and documentation are freely available for download at https://github.com/KijinKims/VirPipe, implemented in Python and Nextflow. Oxford University Press 2023-05-02 /pmc/articles/PMC10191607/ /pubmed/37129547 http://dx.doi.org/10.1093/bioinformatics/btad293 Text en © The Author(s) 2023. Published by Oxford University Press. 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 Applications Note
Kim, Kijin
Park, Kyungmin
Lee, Seonghyeon
Baek, Seung-Hwan
Lim, Tae-Hun
Kim, Jongwoo
Manavalan, Balachandran
Song, Jin-Won
Kim, Won-Keun
VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing
title VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing
title_full VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing
title_fullStr VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing
title_full_unstemmed VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing
title_short VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing
title_sort virpipe: an easy-to-use and customizable pipeline for detecting viral genomes from nanopore sequencing
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10191607/
https://www.ncbi.nlm.nih.gov/pubmed/37129547
http://dx.doi.org/10.1093/bioinformatics/btad293
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