ViMOP: a user-friendly and field-applicable pipeline for untargeted viral genome nanopore sequencing.

ABSTRACT:

Motivation

Untargeted, also known as metagenomic, nanopore sequencing is a powerful tool for virus genomic surveillance, particularly in resource-limited settings and when paired with the portability of the MinION device (Oxford Nanopore Technologies, ONT). However, a major bottleneck for global access is the absence of a user-friendly software capable of efficiently analyzing untargeted nanopore sequencing data to generate high-quality consensus genomes.

Results

We share ViMOP, a pipeline built on our long-term experience in nanopore field sequencing. The pipeline emphasizes field user-friendliness, flexibility and versatility to analyze reads generated directly from human clinical samples. The software assembles de novo contigs, matches contigs to known viral references an

SUBMITTER: Petersen NP 

PROVIDER: S-EPMC12809542 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature