Agent skill · research science · aiskillstore
sragent
Query the Sequence Read Archive (SRA), retrieve scientific publications, and analyze genomics metadata using the SRAgent toolkit. Supports accession conversion (GSE→SRX→SRR), BigQuery metadata queries, manuscript downloads from multiple sources, and scRNA-seq technology identification. Use when working with SRA/GEO datasets, finding publications, or analyzing single-cell sequencing experiments.
Why this skill is useful
Adds executable scripts for accession conversion and metadata extraction that are not commonly found in public documentation.
What it needs
Requires python installed locally. Requires anthropic, core, google, ncbigene, openai account access. About 7k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
SRAgent: Sequence Read Archive Data and Publication Retrieval Overview SRAgent is an agentic workflow system for working with the NCBI Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. It automates literature discovery, metadata extraction, and manuscript retrieval for genomics datasets. Setup Instructions 1. Install SRAgent SRAgent requires Python ≥3.11. Check to see if SRAgent is already installed: If SRAgent is not installed, follow the instructions below. Install using uv: Verify installation: 2. Configure environment variables The following environment variables are required: OPENAIAPIKEY=sk-openai-... Needed to use OpenAI models ANTHROPICAPIKEY=sk-ant-... Needed to use Claude models DYNACONF Needed to switch between Claude and OpenAI models EMAIL=user@example.com Needed for using the Entrez API NCBIAPIKEY=your-ncbi-key Optional for increased rate limits when using the Entrez API COREAPIKEY=your-core-key Optional for paper downloads from the CORE API GCPPROJECTID=your-project-id Needed for using Google BigQuery GOOGLEAPPLICATIONCREDENTIALS=/path/to/key.json Needed for using Google BigQuery Prompt the user to provide the environment variables if they are not already set as environment variables: export MYSECRETVAR=my-secret-value. 3. Configure Settings SRAgent uses a settings file (settings.yml) to configure models and behavior. The default configuration works for most users, but you can customize it. Option A: Use Default Settings No action needed - SRAgent ships with sensible defaults. Option B: Custom Settings File See ./references/example-settings.yml for an example settings file that you can modify as needed. 4. Verify Setup Test your configuration: Core Capabilities 1. Accession Conversion Convert between different genomics database accession formats: GEO Series: GSE → SRA Study (SRP) SRA Study: SRP/PRJNA → SRA Experiments (SRX) SRA Experiment: SRX/ERX → SRA Runs (SRR/ERR) 2. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/sragent