bio-epidemiological-genomics-transmission-inference

bio-epidemiological-genomics-transmission-inference is a Bioinformatics & life sciences skill for AI agents, published by GPTomics in the bioSkills repository on GitHub. Skillspace rates bio-epidemiological-genomics-transmission-inference B (81/100) and it passed the safety scan; the rating is based on static analysis only.

Infers person-to-person transmission from pathogen genomes using outbreaker2, TransPhylo, phybreak, BadTrIP, SCOTTI, BEASTLIER, and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs; MRSA <=15; C. difficile <=2; Klebsiella <=21), models within-host diversity and transmission bottlenecks, integrates contact-tracing data, distinguishes generation from serial interval, and attributes source via Bayesian source attribution (islandR). Use when investigating outbreaks for who-infected-whom, defining SNP-cluster outbreak definitions, accounting for unsampled intermediates, choosing between outbreaker2 (rich epi data) and TransPhylo (genomic-only after a dated phylogeny), running source attribution between host populations, calling HIV-TRACE thresholds appropriate to the local subtype, or distinguishing recent transmission from reactivation in TB or chronic HIV.

Grade
B
Quality
81 / 100
Safety
Passed
GitHub stars
1,025

Unproven: rated by static analysis only, not yet compared head-to-head.

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View source on GitHubGPTomics/bioSkills

Our review

Architecture
100 / 100
Maturity
Structured: ships references or scripts
Security scan
No issues found
License
MIT
Adoption
Adopted by 0 other repositories, in 2 collections

Not checked yet

  • Not judged on the rubric yet (not a contender in its category)
  • No blind task eval yet
  • Scope (portable / vendor / repo-internal) not assessed; only the top of each category is read for scope
  • Sibling files (scripts, references) not fetched; security scan covers SKILL.md only

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