ArticleBioinformatics (Oxford, England)2026
ViMOP: a user-friendly and field-applicable pipeline for untargeted viral genome nanopore sequencing.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed.
- Nosocomial Outbreak of Lassa Fever in Conakry, Guinea, 2022.The Journal of infectious diseases · 2026Article
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Authors and funding
15 authors.
Funding
Abstract
motivationUntargeted, 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.
resultsWe 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 and uses them to assemble consensus genomes. Executed with a single Nextflow command or via the EPI2ME Desktop interface (ONT), results are summarized in an HTML report. ViMOP, through its user-centered design, lowers the barrier to high-quality virus genome reconstruction and advances capacity for genomic surveillance. AVAILABILITY AND IMPLEMENTATION: ViMOP is freely available for non-commercial use (https://github.com/opr-group-bnitm/vimop and https://zenodo.org/records/17913089), along with the associated database (https://zenodo.org/records/17652512), the scripts used to generate it (https://zenodo.org/records/17632662) and benchmarking code (https://zenodo.org/records/17633185).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.