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
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.
Topics & Concepts
Nanopore sequencingMinionPython (programming language)Computer scienceGenomeNanoporePipeline (software)Computational biologyDocumentationSource codeBiologyGeneticsProgramming languageEngineeringGeneChemical engineeringBacteriophages and microbial interactionsGenomics and Phylogenetic StudiesPlant Virus Research Studies