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Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

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Published on: March 11, 2020

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

Kijin Kim¹, Kyungmin Park^2,3, Seonghyeon Lee⁴

¹Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany.

Bioinformatics (Oxford, England)

|May 2, 2023

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.

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