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

Research output: Contribution to journalArticlepeer-review

2 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 languageEnglish
Article numberbtad293
JournalBioinformatics
Volume39
Issue number5
DOIs
Publication statusPublished - 2023 May

Bibliographical note

Funding Information:
This work was supported by Korea Institute of Marine Science & Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries, Korea [20210466]. This study was also funded by Basic Research Program through the National Research Foundation of Korea (NRF) by the Ministry of Education [NRF-2021R1I1A2049607]; and the Korea government (MSIT) [2023R1A2C2006105].

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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