nf-UnO

nf-UnO identifies novel pathogens from metagenomic shotgun sequencing of epidemiologically related foodborne outbreak specimens.

Key Features:

• Metagenomic Co-assembly: nf-UnO performs metagenomic co-assembly of multiple outbreak specimens to reconstruct genomes.
• Multiple Binning Programs: The pipeline employs multiple binning programs to separate metagenomic assembled genomes.
• Read Mapping to Metagenomically Assembled Genomes: Reads are mapped back to metagenomically assembled genomes to detect potential etiological agents found in common across outbreak specimens.
• MIDAS2 Integration: nf-UnO uses MIDAS2 for metagenomic analysis steps.

Scientific Applications:

• Novel Pathogen Detection: nf-UnO detects potential etiological agents from metagenomic shotgun sequencing of foodborne outbreak specimens.
• Foodborne Outbreak Investigation: The pipeline identifies pathogens shared across epidemiologically related outbreak specimens.

Methodology:

nf-UnO is implemented in Nextflow and uses MIDAS2, metagenomic co-assembly, multiple binning programs, and read mapping to metagenomically assembled genomes.