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

Kijin Kim; Kyungmin Park; Seonghyeon Lee; Seung Hwan Baek; Tae Hun Lim; Jongwoo Kim; Balachandran Manavalan; Jin Won Song; Won Keun Kim

doi:10.1093/bioinformatics/btad293

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

Kijin Kim
, Kyungmin Park
, Seonghyeon Lee
, Seung Hwan Baek
, Tae Hun Lim
, Jongwoo Kim
, Balachandran Manavalan
, Jin Won Song
, Won Keun Kim

Department of Integrative Biotechnology

Saarland University
Korea University
Hallym University

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

Abstract

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.

Original language	English
Article number	btad293
Journal	Bioinformatics
Volume	39
Issue number	5
DOIs	https://doi.org/10.1093/bioinformatics/btad293
State	Published - May 2023

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10.1093/bioinformatics/btad293

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

abstract = "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.",

author = "Kijin Kim and Kyungmin Park and Seonghyeon Lee and Baek, \{Seung Hwan\} and Lim, \{Tae Hun\} and Jongwoo Kim and Balachandran Manavalan and Song, \{Jin Won\} and Kim, \{Won Keun\}",

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AU - Lee, Seonghyeon

AU - Baek, Seung Hwan

AU - Lim, Tae Hun

AU - Kim, Jongwoo

AU - Manavalan, Balachandran

AU - Song, Jin Won

AU - Kim, Won Keun

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AB - 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.

UR - https://www.scopus.com/pages/publications/85160681735

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DO - 10.1093/bioinformatics/btad293

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

Abstract

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