Speaker
Description
We developed ViMOP (Virus Metagenomics Outbreak Pipeline), a Nextflow pipeline based on our long-term experience in nanopore field sequencing in small stationary and mobile laboratories in Sub-Saharan Africa. ViMOP is designed to be robust and easy to use on a laptop for the automated analysis of nanopore reads generated directly from human clinical samples. The pipeline performs de novo assembly of contigs, identifies viral references through a database search, and uses them to reconstruct consensus genomes. The workflow can be executed with a single Nextflow command or run entirely without command-line interaction through the EPI2ME Desktop interface, and results are summarized in a simple yet comprehensive HTML report. It is available on GitHub via: github.com/opr-group-bnitm/vimop.