Pathogen-agnostic antiviral resistance profiling from consensus sequences or VCF-derived variants.

Tip

Built your own database. Its super simple.

One harmonized report that classifies mutations and assists diagnostic interpretation against curated project databases. Comes as a CLI or a WebApp. Everything is open-source. Contributions are welcome!

Dokumentation · WebApp (live) · Installation · Databases

Highlights

• Framework for genotypic antiviral resistance analysis — not limited to a single pathogen
• Get auto-curated project databases with built-in QC and reference normalization
• Amino-acid-centered rule matching with combination-rule support (AND, OR, NOT, XOR)
• Pre-ported maintained databases available via respro databases --download
• CLI-first design for workflow integration; companion WebApp for interactive use
• Deterministic report regeneration from stored results

Quick start

Install the CLI via conda (recommended):

conda create -n respro
conda activate respro
conda install bioconda::respro

Install via Docker (BioContainers):

docker pull quay.io/biocontainers/respro

Install via pip:

git clone https://github.com/the-foxlab/ResistanceProfiler
pip install -e ".[dev]"

Download a maintained database (e.g. herpesDRG):

respro databases --list
respro databases --download herpesdrg --output my_folder/

Profile:

respro fasta --project my_folder/herpesdrg.db --fasta sample.fasta --output results/

or

respro vcf --project my_folder/herpesdrg.db --vcf sample.vcf --ref-fasta ref.fasta --output results/

→ Full guide: Installation · Quickstart · CLI Reference

Web app (host the complete WebApp via docker)

git clone https://github.com/the-foxlab/ResistanceProfiler
docker compose -f docker-compose.web.yml up --build

Open at http://127.0.0.1:8000/

Prefer the prebuilt CI image (no local build)? It's published to GHCR on every push to master:

docker pull ghcr.io/the-foxlab/resistanceprofiler:latest

See the webapp docs for pulling a specific tag, authenticated pulls for private packages, and the egress requirements for a server that fetches images at runtime.

→ Web app documentation

License

AGPL v3.0 — source code only. External databases and references may carry separate licenses.