ViMOP

ViMOP analyzes untargeted nanopore sequencing reads from human clinical samples to assemble de novo contigs, match them to known viral references, and generate high-quality consensus genomes for virus genomic surveillance.

Key Features:

• De novo assembly: Assembles reads into contigs without prior reference genome information.
• Reference matching: Matches assembled contigs to known viral references from an associated database.
• Consensus genome assembly: Uses matched references to assemble high-quality consensus genomes.
• Nextflow execution: Runs with a single Nextflow command for workflow management.
• HTML report generation: Summarizes results in an HTML report.

Scientific Applications:

• Virus genomic surveillance: Enables genomic monitoring of viruses in resource-limited settings using the MinION device (Oxford Nanopore Technologies, ONT).
• Metagenomic virus detection: Analyzes untargeted nanopore sequencing data directly from human clinical samples to identify and reconstruct viral genomes.

Methodology:

The pipeline assembles de novo contigs from nanopore reads, matches contigs to known viral references, and uses matched references to assemble consensus genomes.