Individual skill
genomic-epidemiology
Pathogen genomics for epidemiology — phylogenetics of outbreaks, transmission inference, and variant surveillance.
skills/genomic-epidemiology/SKILL.md
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## Overview
genomic-epidemiology uses pathogen genome sequences to answer epidemiologic questions: who
infected whom, where a lineage came from, how fast it's spreading, and whether a new variant
matters. It combines phylogenetics with field epidemiology — sequences alone rarely answer
anything without epidemiologic metadata (dates, locations, exposures).
## When to use
- Outbreak phylogenetics: lineage assignment, cluster identification.
- Transmission inference: combining genomics with contact tracing.
- Molecular-clock dating: when did a lineage emerge or enter a region?
- Variant surveillance: detecting and characterizing concerning lineages.
- Phylodynamics: estimating Re and growth rates from sequences.