Core Capabilities

Pangenome-Powered Classification

This is the central function of Virus-Mapper. Instead of just guessing if a variant is real, the tool directly checks for its presence in the pangenome graph. The result is a clear, unambiguous classification in your VCF INFO field.

• KNOWN: The exact alternate allele exists in the graph.
• NOVEL: The alternate allele is not found in the graph.

# Your input VCF record
chr1    12345   .   A   G   .   .   ...

# The annotated output from Virus-Mapper
chr1    12345   .   A   G   .   .   G_ALLELE_STATE=KNOWN;...

Haplotype & Sample Resolution

Knowing a variant is present in the pangenome is only half the story. Virus-Mapper tells you exactly which samples or reference paths in the graph carry that variant.

This is critical for tracking variant inheritance, identifying cohort-specific alleles, or confirming a variant's presence on an emerging viral lineage.

# An output record showing the allele is present in two haplotypes
... G_ALLELE_STATE=KNOWN;G_HAPLOTYPES=HG002,NA19240

Powerful & Intuitive Filtering

Zero in on the variants that matter. Virus-Mapper includes a point-and-click filter builder that lets you construct complex queries without needing to memorize syntax.

For power users, it supports standard VCF expressions (like those used in `bcftools`), giving you full control to filter by quality, INFO fields, or any other metric before the pangenome analysis begins.

# Build complex filters with a simple UI
# Example: Find high-quality variants with sufficient read depth
QUAL >= 50 && INFO.DP > 20

Integrated Viral Gene Annotation

When working with viral genomes, context is everything. With the annotation feature enabled, Virus-Mapper automatically cross-references variant positions against the NCBI RefSeq viral database.

Instantly see if your variant falls within a critical gene (like Spike) or another feature, adding a crucial layer of biological context to your results.

# A variant falling within the Spike (S) gene's coding sequence (CDS)
... G_ALLELE_STATE=KNOWN;V_GENE=S;V_FEAT=CDS

Privacy by Design: Your Data Stays Yours

In an era of cloud computing, Virus-Mapper takes a different approach. All analysis—from file parsing to pangenome interrogation—happens entirely on your local machine within the secure Docker container.

Your sensitive genomic data is never uploaded, transmitted, or shared. This local-first architecture guarantees complete confidentiality and control, making it suitable for clinical, proprietary, or any other sensitive research.

[ Your Computer ]
   |
   +-- [ Docker Container ]
   |      |
   |      +-- [ Virus-Mapper App ] <--> [ Your Local Files ]
   |
   (No data ever leaves)
   x---------------------> [ The Internet ]

Engineered for Speed & Scale 🚀

Built in Rust, Virus-Mapper is designed to maximize performance by using all available CPU cores and processing data efficiently.

• Parallel Processing: The analysis of VCF records is automatically distributed across all your computer's CPU cores, dramatically reducing analysis time.
• In-Memory Graph: The entire pangenome graph (GFA/ODGI) is loaded into RAM for the fastest possible access. Multi-gigabyte graphs are fully supported, provided you have enough available RAM (typically 1.5x-2x the ODGI file size).

[ VCF File ] ----> | CPU 1: Process chunk 1 | ----> [ Results ]
                 | CPU 2: Process chunk 2 |         (in RAM)
                 | CPU 3: Process chunk 3 |
                 | ...                    |
                 | CPU N: Process chunk N |

Powered by a High-Performance Core

Virus-Mapper's speed and pangenome capabilities are made possible by the state-of-the-art ODGI library. To bring this power to a modern web application, we developed odgi-ffi.

This new Rust crate serves as a safe, high-performance bridge between the Rust backend and the C++ ODGI library. This architecture gives you the best of both worlds: the memory safety and concurrency of Rust with the battle-tested performance of ODGI's pangenome algorithms.

Learn more about the crate here: odgi-ffi on crates.io

[ Virus-Mapper Web App (Rust) ]
           ↓
[ odgi-ffi (Safe Rust Bridge) ]
           ↓
[ ODGI Core Engine (C++) ]