propenster/prrsifier repository overview

⁠prrsifier

PRRSV ORF5 Evolutionary Lineage and Genetic Clade Classification

A fast, self-contained command-line tool for classifying porcine reproductive and respiratory syndrome virus (PRRSV) ORF5 sequences into their known evolutionary lineages.

⁠Motivation

PRRSV is one of the most economically damaging pathogens in the global swine industry. Its ORF5 gene — encoding the GP5 envelope glycoprotein — evolves rapidly and is the standard target for molecular epidemiology, lineage tracking, and vaccine-strain discrimination.

Existing classification tools exist (Nextclade, PRRS-Loom), but they are either web-only or lock users into a fixed reference model. prrsifier is different: it is self-hosted, open-source, and lets you swap in your own reference set without retraining anything. Every classification comes with a confidence score and full traceability — you can trace any assignment back to the specific reference sequence it matched, and immediately see which queries are genuinely novel versus merely under-sampled.

Built for veterinary diagnostic labs, surveillance programs, and researchers who need reproducible lineage assignment.

⁠How It Works

Each query is assigned the lineage of its nearest reference sequence in the tree. The confidence metric measures how much closer the nearest neighbor is compared to the second-nearest:

confidence = (second_dist - nearest_dist) / nearest_dist

• confidence >= 0.5 → strong, unambiguous assignment
• 0.1 <= confidence < 0.5 → moderate; query sits between two clusters
• confidence < 0.1 → novel candidate; flagged for wet-lab characterization

⁠Stack

The classifier itself is written in Rust — no Python dependency at runtime. The heavy lifting (alignment, tree inference) is delegated to the standard tools the field already trusts.

⁠Usage

⁠With Docker (recommended)

docker pull propenster/prrsifier:0.1.0

docker run --rm -v "$PWD:/work" propenster/prrsifier:0.1.0 \
  -i /work/queries.fa \
  -o /work/results.tsv \

⁠From source

git clone https://github.com/propenster/prrsifier.git
cd prrsifier
make refs blastdb classifier
./classifier/target/release/prrsifier \
  -i queries.fa \
  -o results.tsv \

⁠Options

-i, --input <FILE>           Input FASTA of query ORF5 sequences
-o, --output <FILE>          Output TSV (default: output.tsv)
-d, --data-dir <DIR>         Root dir containing prrsv1/ and prrsv2/ (default: data)
-c, --min-confidence <FLOAT> Confidence threshold for "Novel" flagging (default: 0.10)
-t, --threads <N>            Threads for BLAST and MAFFT (default: 1)
    --workdir <DIR>          Keep intermediate files for debugging

⁠Output format

query_id    species  lineage  nearest_ref  nearest_dist  second_ref   second_dist  confidence  flag
OR293404    prrsv2   L1A      OR293404     0.0           EU756373     0.0135...    1.0         Classified

⁠Reference Sets

prrsifier ships with curated ORF5 reference sets derived from peer-reviewed nomenclature:

⁠Extensibility

The reference set is plain FASTA + TSV. To add a new variant, sublineage, or vaccine strain:

Append the sequence to data//reference_clean.fasta

Add a matching row to data//reference_metadata.tsv

Rebuild the BLAST database: make blastdb

No model weights, no retraining, no black box.

Citation If prrsifier contributes to your work, please cite the preprint: Olusegun, F. (2026). prrsifier: an extensible, self-hosted PRRSV ORF5 lineage classifier with auditable provenance and confidence scoring. bioRxiv. (link once posted)

References:

Yim-im, W., et al. (2023). Refining PRRSV-2 genetic classification based on global ORF5 sequences. Microbiol Spectr.

Yim-im, W., et al. (2025). Global PRRSV-1 ORF5 lineage classification. Vet Microbiol.

Chandra et al. 2025 — describe SDRS as the state of the art for U.S. PRRSV surveillance

Zeller et al. 2024 — Nextclade PRRSV-2

Zeller et al. 2023 — ClassLog

Vander Waal et al. 2024 — variant classification (PRRS-Loom)

Paploski et al. 2021 — sub-lineage dynamics (background)

⁠License

MIT © 2026 Faith (propenster) Olusegun

Acknowledgements Built on the shoulders of the open-source bioinformatics community — in particular the developers of BLAST+, MAFFT, FastTree, and the researchers whose published nomenclature made the reference curation possible.