scientific-infectious-disease

Integrates pathogen genomics and epidemiology data for outbreak analysis and molecular typing workflows.

3|1|Updated Feb 11, 2026

Search Tags:#genomics #modeling #typing #epidemiology #phylogenetics #outbreak #amr

Ready to run

npx skills add https://github.com/nahisaho/satori --skill scientific-infectious-disease

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: scientific-infectious-disease
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-infectious-disease
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-infectious-disease

SYSTEM DOCUMENTATION & REQUIREMENTS

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.

Frequently Asked Questions about scientific-infectious-disease

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I integrate pathogen genomics and epidemiology data for outbreak analysis?▼

You can perform WGS-based typing by providing pathogen genome data in FASTQ or FASTA formats. The pipeline processes WGS data to execute MLST, cgMLST, and SNP typing for lineage tracing during outbreak investigations.

Can I use WGS data to detect AMR genes and resistance profiles?▼

Yes, the pipeline detects AMR genes and resistance profiles from sequencing data. This AMR detection applies molecular typing workflows to identify resistance genes and inform treatment strategies during an outbreak.

How do I run compartment models like SIR or SEIR for transmission modeling?▼

You can run compartment models with configurable parameters to simulate pathogen spread. The pipeline executes SIR and SEIR models to forecast outbreak size and evaluate interventions based on integrated epidemiology data.

What is the best way to combine molecular typing and phylogenetics for outbreak investigations?▼

The best way to combine molecular typing and phylogenetics for outbreak investigations is using an integrated genomics pipeline. It constructs phylogenies from WGS data and infers transmission networks to identify transmission routes during hospital outbreaks.

Does this outbreak analysis pipeline require specific input formats for sequencing data?▼

Yes, the outbreak analysis pipeline requires pathogen genome data in FASTQ or FASTA formats. You must provide sequencing data in these formats to run the end-to-end pipeline for typing results, phylogenies, and transmission estimates.