bio-workflows-outbreak-pipeline
OfficialFrom isolates to transmission networks.
Data & Analytics#phylodynamics#outbreak-investigation#genomic-epidemiology#mlst#amr-surveillance#transmission-inference#treetime
Authorstellaromics
Version1.0.0
Installs0
System Documentation
What problem does it solve?
End-to-end orchestration of pathogen outbreak investigations using genome data, enabling seamless MLST typing, AMR surveillance, phylodynamics dating, and transmission inference to produce actionable outbreak insights.
Core Features & Use Cases
- End-to-end genomic outbreak pipeline: MLST typing, AMR detection, core-genome alignment, phylogenetics, phylodynamics, and transmission inference.
- Outputs include dated phylogeny, transmission network, and R0 estimates to inform outbreak control measures.
- Use Case: Hospital outbreaks characterized by isolates with dates and genomes to reconstruct who infected whom and the outbreak timeline.
Quick Start
Provide your isolate genomes and collection dates to run the end-to-end outbreak pipeline and generate a dated phylogeny and transmission network.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
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Please help me install this Skill: Name: bio-workflows-outbreak-pipeline Download link: https://github.com/stellaromics/fast-bioinfo/archive/main.zip#bio-workflows-outbreak-pipeline Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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