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^*

^*Corresponding author for this work

Department of Biomedical Sciences

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

11 Citations (Scopus)

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
Publication status	Published - 2023 May

Bibliographical note

Publisher Copyright:
© The Author(s) 2023. Published by Oxford University Press.

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btad293

Cite this

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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.",

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doi = "10.1093/bioinformatics/btad293",

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AU - Kim, Kijin

AU - Park, Kyungmin

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

PY - 2023/5

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N2 - 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.

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

U2 - 10.1093/bioinformatics/btad293

DO - 10.1093/bioinformatics/btad293

M3 - Article

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ER -

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

Abstract

Bibliographical note

ASJC Scopus subject areas

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