Early Access Program Now Open

Go Beyond the Reference Genome.

Virus-Mapper unlocks the full story of your viral data. Instantly classify variants against a pangenome to discover novel mutations and track lineage-defining haplotypes with unprecedented clarity.

Get Early Access

A screenshot of the Virus-Mapper application UI showing the file selection, validation checks, and results table.

From Raw Data to Actionable Insight

STEP 1

Upload Your Data

Provide your VCF file, a pangenome graph (GFA/ODGI), and its corresponding reference FASTA. Our pre-flight checks ensure data compatibility.

STEP 2

Run Analysis

Our high-performance Rust engine interrogates every variant against the graph, leveraging the power of ODGI for maximum speed and efficiency.

STEP 3

Get Annotated Results

Download an enriched VCF file with clear "Known" vs. "Novel" classifications, haplotype information, and optional viral gene annotations.

Core Capabilities

Novel Variant Detection

Go beyond simple annotation and determine if your variant is truly novel or just missing from the linear reference.

Haplotype Resolution

For known variants, Virus-Mapper identifies which specific samples or paths within your pangenome contain the alternate allele.

Robust SV Support

Accurately process and classify complex structural variants, including deletions, insertions, and duplications. (Note: INV support is limited).

See All Features

Ready to Join the Program? 🚀

Get started with our secure, local-first Docker installation and see what you've been missing in your variant data.

View Installation Guide