scientific-infectious-disease
CommunityIntegrated genomics for outbreak insight.
Authornahisaho
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Pathogen genomics and epidemiology data are often siloed, hindering rapid outbreak investigations and containment planning.
Core Features & Use Cases
- Genome typing & phylogenetics: WGS-based typing (MLST, cgMLST, SNP) and phylogenetic analysis for lineage tracing.
- AMR detection & molecular typing: Detection of AMR genes and resistance profiles to inform treatment strategies.
- Outbreak transmission & mathematical modeling: Transmission network inference and compartment models (SIR/SEIR) to simulate spread and evaluate interventions.
- Use Case: During a hospital outbreak, combine pathogen genomics with epidemiological models to identify transmission routes and forecast outbreak size.
Quick Start
Provide pathogen genome data in FASTQ/FASTA formats and run the end-to-end integrated pipeline to obtain typing results, phylogenies, and transmission estimates.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: scientific-infectious-disease Download link: https://github.com/nahisaho/satori/archive/main.zip#scientific-infectious-disease Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
Agent Skills Search Helper
Install a tiny helper to your Agent, search and equip skill from 471,000+ vetted skills library on demand.