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robinbarvaag
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ena-database

Retrieve nucleotide sequences, FASTQ reads, and genome assemblies from ENA via REST APIs.

Updated Jan 10, 2026
Search Tags:#api#bioinformatics#genomics#sequence retrieval#ena#nucleotide
One-click install
npx skills add https://github.com/robinbarvaag/poynt --skill ena-database-robinbarvaag
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ena-database
Source: https://github.com/robinbarvaag/poynt/tree/main/.github/skills/ena-database
Command: npx skills add https://github.com/robinbarvaag/poynt --skill ena-database-robinbarvaag

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides programmatic access to the European Nucleotide Archive (ENA), enabling users to retrieve DNA/RNA sequences, raw reads, and genome assemblies for bioinformatics pipelines.

Core Features & Use Cases

  • Data Retrieval: Fetch nucleotide sequences, raw sequencing reads (FASTQ), and genome assemblies by accession.
  • Metadata Search: Query ENA for studies, samples, and experiments based on various criteria.
  • API Integration: Utilize REST APIs for advanced searching and data access.
  • Use Case: A researcher needs to download all FASTQ files for a specific study accession to perform downstream RNA-Seq analysis.

Quick Start

Use the ena-database skill to retrieve raw sequencing reads for accession ERR123456.

Frequently Asked Questions about ena-database

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

FAQPage Schema
How do I retrieve raw sequencing reads and genome assemblies from the European Nucleotide Archive?▼

To retrieve raw sequencing reads and genome assemblies from the European Nucleotide Archive, you can use this Skill to fetch data via accession numbers. It supports REST APIs and FTP for comprehensive programmatic access.

Can I query ENA metadata for specific studies, samples, and experiments?▼

Yes, you can query ENA metadata for studies, samples, and experiments. The Skill integrates with the ENA Portal API, Browser API, and Taxonomy API to support advanced searching based on specific criteria.

What is the best way to download FASTQ files for a specific ENA study accession?▼

The best way to download FASTQ files for a specific study accession is using this Skill's data retrieval capabilities. It enables programmatic access to fetch raw reads directly for downstream bioinformatics pipelines.

Does this ENA retrieval tool support REST API integration for genomics pipelines?▼

Yes, this ENA retrieval tool supports REST API integration for genomics pipelines. It utilizes the Portal API, Browser API, and Taxonomy API to enable comprehensive sequence retrieval and data querying.

When do I need programmatic access to the European Nucleotide Archive?▼

You need programmatic access to the European Nucleotide Archive when automating bioinformatics pipelines to retrieve DNA/RNA sequences, raw reads, or genome assemblies. It allows fetching data by accession via APIs.

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