About WINGS
WINGS is a portable Snakemake workflow for genomic characterization, bioinformatics analysis, and surveillance of avian influenza A viruses from wild-bird samples sequenced using Oxford Nanopore technologies.
The workflow integrates read preprocessing, influenza assembly, segment-level quality assessment, consensus polishing, variant calling, subtype screening, genotype assignment, annotation, and interactive reporting to support genomic epidemiology and wildlife disease surveillance.
Pipeline capabilities
Nanopore sequencing
Processes Oxford Nanopore reads for influenza A genomic analysis.
Genome assembly
Uses CDC IRMA for influenza genome assembly and segment recovery.
Genomic characterization
Performs consensus polishing, variant analysis, subtype screening, genotype assignment, and sequence annotation.
Surveillance reporting
Generates sample-level and sequencing-run HTML reports for reviewing genomic surveillance results.
Genomic epidemiology and surveillance
WINGS was designed to support genomic epidemiology of avian influenza viruses detected through surveillance of wild birds. The workflow provides a reproducible path from raw sequencing reads to curated genomic outputs that can be used in downstream phylogenetic, phylodynamic, and epidemiologic analyses.
Local-first reporting
Sequencing results remain on the user's computer or analysis system. WINGS includes a local report server for navigating run-level and sample-level reports without publishing sequencing data to this site.
After generating the reports, launch the local viewer from the repository root with:
./view_reports.sh
Pandemic ESCAPE Center
WINGS was developed in support of the Pandemic ESCAPE Center and its efforts in pathogen surveillance, sequencing, bioinformatics, and understanding the emergence and spread of infectious disease threats.