VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 37129547.
- Also identified by DOI 10.1093/bioinformatics/btad293 and PMC identifier 10191607.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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. VirPipe source code and documentation are freely available for download at https://github.com/KijinKims/VirPipe, implemented in Python and Nextflow.
Medical subject headings
- Nanopore Sequencing
- Nanopores