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

Bioinformatics. 2023 May 4;39(5):btad293. doi: 10.1093/bioinformatics/btad293.

Authors

Kijin Kim¹, Kyungmin Park^{2

3}, Seonghyeon Lee⁴, Seung-Hwan Baek⁵, Tae-Hun Lim⁴, Jongwoo Kim^{2

3}, Balachandran Manavalan⁶, Jin-Won Song^{2

3}, Won-Keun Kim^{4

5}

Affiliations

¹ Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany.
² Department of Biomedical Sciences, BK21 Graduate Program, Korea University College of Medicine, Seoul 02841, Republic of Korea.
³ Department of Microbiology, Korea University College of Medicine, Seoul 02841, Republic of Korea.
⁴ Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea.
⁵ Institute of Medical Research, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea.
⁶ Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea.

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.

Availability and implementation: VirPipe source code and documentation are freely available for download at https://github.com/KijinKims/VirPipe, implemented in Python and Nextflow.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome, Viral
High-Throughput Nucleotide Sequencing
Nanopore Sequencing*
Nanopores*
Software