VirPipe: an easy and robust pipeline for detecting customized viral genomes obtained by Nanopore sequencing 

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

Abstract

Summary

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

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

Supplementary information

Supplementary data are available at Bioinformatics online.

Issue Section:

APPLICATIONS NOTE

Associate Editor: Can Alkan  

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