[{"_1":2,"_184":-5,"_185":-5},"loaderData",{"_3":4,"_18":19,"_26":27,"_157":158},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16,"_17":11},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","dockerRebrandTour","routes/_layout",{"_20":-5,"_21":22,"_23":22,"_24":11,"_25":22},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_28":29,"_30":-5,"_31":11,"_32":11,"_33":34,"_35":36,"_37":-5,"_38":11,"_39":40,"_89":-5,"_90":91,"_145":-5,"_146":11,"_147":22,"_148":11,"_149":11,"_150":-5,"_151":11,"_152":-5,"_153":154,"_155":92,"_156":-7},"canonicalUrl","https://hub.docker.com/r/propenster/prrsifier/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","propenster","reponame","prrsifier","cloudBuildSource","isAutobuildsAvailable","repo",{"_41":42,"_43":44,"_46":47,"_48":49,"_50":11,"_51":52,"_53":54,"_55":56,"_58":36,"_33":34,"_59":60,"_61":-5,"_62":63,"_64":65,"_66":67,"_68":-5,"_69":63,"_70":71,"_72":11,"_73":34,"_74":75,"_80":11,"_81":82,"_86":34,"_87":88},"categories",[],"content_types",[45],"image","date_registered","2026-10-12T16:49:19.186926Z","description","PRRSV ORF5 Evolutionary Lineage and Genetic Clade Classification","is_private","last_updated","2026-10-12T20:52:19.398811Z","last_modified","2026-10-12T20:55:49.250654Z","media_types",[57],"application/vnd.oci.image.index.v1+json","name","pull_count",210,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# prrsifier\n\n**PRRSV ORF5 Evolutionary Lineage and Genetic Clade Classification**\n\nA fast, self-contained command-line tool for classifying porcine reproductive and respiratory syndrome virus (PRRSV) ORF5 sequences into their known evolutionary lineages.\n\n---\n\n## Motivation\n\nPRRSV 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.\n\nExisting 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.\n\nBuilt for veterinary diagnostic labs, surveillance programs, and researchers who need reproducible lineage assignment.\n\n---\n\n## How It Works\n\n![Pipeline Architecture](prrsifier.jpg)\n\nEach 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:\n\n`confidence = (second_dist - nearest_dist) / nearest_dist`\n\n* **`confidence >= 0.5`** → strong, unambiguous assignment\n* **`0.1 <= confidence < 0.5`** → moderate; query sits between two clusters\n* **`confidence < 0.1`** → novel candidate; flagged for wet-lab characterization\n\n---\n\n## Stack\n\n| Component | Role |\n|---|---|\n| **Rust** | Orchestration, Newick parsing, patristic distances, classification logic |\n| **BLAST+** | Species discrimination against reference databases |\n| **MAFFT** | Multiple sequence alignment |\n| **FastTree** | Approximate maximum-likelihood tree inference |\n| **Conda** | Reproducible environment for bioinformatics tools |\n| **Docker** | Self-contained, portable runtime |\n\nThe 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.\n\n---\n\n## Usage\n\n### With Docker (recommended)\n\n```bash\ndocker pull propenster/prrsifier:0.1.0\n\ndocker run --rm -v \"$PWD:/work\" propenster/prrsifier:0.1.0 \\\n -i /work/queries.fa \\\n -o /work/results.tsv \\\n```\n\n### From source\n\n```bash\ngit clone https://github.com/propenster/prrsifier.git\ncd prrsifier\nmake refs blastdb classifier\n./classifier/target/release/prrsifier \\\n -i queries.fa \\\n -o results.tsv \\\n ``` \n### Options\n\n```text\n-i, --input Input FASTA of query ORF5 sequences\n-o, --output Output TSV (default: output.tsv)\n-d, --data-dir Root dir containing prrsv1/ and prrsv2/ (default: data)\n-c, --min-confidence Confidence threshold for \"Novel\" flagging (default: 0.10)\n-t, --threads Threads for BLAST and MAFFT (default: 1)\n --workdir Keep intermediate files for debugging\n```\n\n### Output format\n\n```text\nquery_id species lineage nearest_ref nearest_dist second_ref second_dist confidence flag\nOR293404 prrsv2 L1A OR293404 0.0 EU756373 0.0135... 1.0 Classified\n```\n\n| Column | Meaning |\n|---|---|\n| `query_id` | Original sequence identifier |\n| `species` | PRRSV-1 or PRRSV-2 |\n| `lineage` | Assigned lineage (e.g. L1A, L8C, L1.6) |\n| `nearest_ref` | Accession of the closest reference sequence |\n| `nearest_dist` | Patristic distance to that reference |\n| `second_ref` | Accession of the second-closest reference |\n| `second_dist` | Patristic distance to that reference |\n| `confidence` | Ratio metric (see above) |\n| `flag` | `Classified` or `Novel/Unclassified` |\n\n### Reference Sets\nprrsifier ships with curated ORF5 reference sets derived from peer-reviewed nomenclature:\n\n| Species | Sequences | Lineages | Source |\n|---|---|---|---|\n| **PRRSV-1** | 955 | 25 | Yim-im et al. 2025 |\n| **PRRSV-2** | 1,100 | 32 | Yim-im & Zhang 2023 |\nBoth sets span all major lineages, sublineages, and commercial vaccine strains. The reference FASTAs and metadata TSVs are in data/, and can be replaced with your own curated panel — no retraining required.\n\n### Extensibility\nThe reference set is plain FASTA + TSV. To add a new variant, sublineage, or vaccine strain:\n\nAppend the sequence to data//reference_clean.fasta\n\nAdd a matching row to data//reference_metadata.tsv\n\nRebuild the BLAST database: make blastdb\n\nNo model weights, no retraining, no black box.\n\nCitation\nIf prrsifier contributes to your work, please cite the preprint:\nOlusegun, F. (2026). prrsifier: an extensible, self-hosted PRRSV ORF5 lineage classifier with auditable provenance and confidence scoring. bioRxiv. (link once posted)\n\nReferences:\n\nYim-im, W., et al. (2023). Refining PRRSV-2 genetic classification based on global ORF5 sequences. Microbiol Spectr.\n\nYim-im, W., et al. (2025). Global PRRSV-1 ORF5 lineage classification. Vet Microbiol.\n\nChandra et al. 2025 — describe SDRS as the state of the art for U.S. PRRSV surveillance\n\nZeller et al. 2024 — Nextclade PRRSV-2\n\nZeller et al. 2023 — ClassLog\n\nVander Waal et al. 2024 — variant classification (PRRS-Loom)\n\nPaploski et al. 2021 — sub-lineage dynamics (background)\n\n### License\nMIT © 2026 Faith (propenster) Olusegun\n\nAcknowledgements\nBuilt 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.\n","has_starred","hub_user","immutable_tags_settings",{"_76":11,"_77":78},"enabled","rules",[79],".*","is_automated","permissions",{"_83":22,"_84":11,"_85":11},"read","write","admin","user","storage_size",1336550359,"orgData","recentTags",[92,138],{"_93":45,"_94":95,"_96":97,"_98":99,"_100":101,"_102":103,"_51":126,"_127":95,"_128":34,"_129":57,"_58":130,"_131":132,"_133":134,"_135":126,"_136":67,"_137":22},"content_type","creator",12520829,"digest","sha256:13b08e1c308e7c83a85d5a84eba17d1dd502da11251029d21aa42af03e1c7f05","full_size",1334588584,"id",1345771302,"images",[104,120],{"_105":106,"_96":107,"_108":109,"_110":111,"_112":113,"_114":115,"_116":109,"_117":-5,"_118":99,"_64":67,"_119":-5},"architecture","amd64","sha256:d47bd4f6cf08bf44ae0274bfa07da7e12899659fd7390e7738f20d93bed1f8d4","features","","last_pulled","2026-10-14T21:14:50.388260043Z","last_pushed","2026-10-12T20:52:07.707176174Z","os","linux","os_features","os_version","size","variant",{"_105":121,"_96":122,"_108":109,"_110":123,"_112":124,"_114":121,"_116":109,"_117":-5,"_118":125,"_64":67,"_119":-5},"unknown","sha256:05ab98be398ddfabee5db813af5bcde005b41596843a5eced5326dcafef65583","2026-10-14T21:17:41.339572443Z","2026-10-12T20:52:07.697016511Z",1672,"2026-10-12T20:52:19.030019Z","last_updater","last_updater_username","media_type","latest","repository",32853883,"tag_last_pulled","2026-10-15T03:53:10.931950892Z","tag_last_pushed","tag_status","v2",{"_93":45,"_94":95,"_96":97,"_98":99,"_100":139,"_102":140,"_51":143,"_127":95,"_128":34,"_129":57,"_58":144,"_131":132,"_133":134,"_135":143,"_136":67,"_137":22},1345771180,[141,142],{"_105":106,"_96":107,"_108":109,"_110":111,"_112":113,"_114":115,"_116":109,"_117":-5,"_118":99,"_64":67,"_119":-5},{"_105":121,"_96":122,"_108":109,"_110":123,"_112":124,"_114":121,"_116":109,"_117":-5,"_118":125,"_64":67,"_119":-5},"2026-10-12T20:52:13.364844Z","0.1.0","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxRunInCloud","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"selectedTag","attestationsUrl","routes/_layout.r.$namespace.$reponame.tags",{"_39":159,"_166":167,"_153":182,"_183":11},{"_41":160,"_43":161,"_46":47,"_48":49,"_50":11,"_51":52,"_53":54,"_55":162,"_58":36,"_33":34,"_59":60,"_61":-5,"_62":63,"_64":65,"_66":67,"_68":-5,"_69":63,"_70":71,"_72":11,"_73":34,"_74":163,"_80":11,"_81":165,"_86":34,"_87":88},[],[45],[57],{"_76":11,"_77":164},[79],{"_83":22,"_84":11,"_85":11},"tags",{"_168":169,"_170":-5,"_171":-5,"_172":173},"count",2,"next","previous","results",[174,178],{"_93":45,"_94":95,"_96":97,"_98":99,"_100":101,"_102":175,"_51":126,"_127":95,"_128":34,"_129":57,"_58":130,"_131":132,"_133":134,"_135":126,"_136":67,"_137":22},[176,177],{"_105":106,"_96":107,"_108":109,"_110":111,"_112":113,"_114":115,"_116":109,"_117":-5,"_118":99,"_64":67,"_119":-5},{"_105":121,"_96":122,"_108":109,"_110":123,"_112":124,"_114":121,"_116":109,"_117":-5,"_118":125,"_64":67,"_119":-5},{"_93":45,"_94":95,"_96":97,"_98":99,"_100":139,"_102":179,"_51":143,"_127":95,"_128":34,"_129":57,"_58":144,"_131":132,"_133":134,"_135":143,"_136":67,"_137":22},[180,181],{"_105":106,"_96":107,"_108":109,"_110":111,"_112":113,"_114":115,"_116":109,"_117":-5,"_118":99,"_64":67,"_119":-5},{"_105":121,"_96":122,"_108":109,"_110":123,"_112":124,"_114":121,"_116":109,"_117":-5,"_118":125,"_64":67,"_119":-5},[],"canDeleteTags","actionData","errors"]

propenster/prrsifier

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