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ena-database

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

Updated Mar 10, 2026
Search Tags:#bioinformatics#genomics#data retrieval#ena#fastq#nucleotide sequence
One-click install
npx skills add https://github.com/Yezez9/Research-Agent --skill ena-database-yezez9
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ena-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/ena-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill ena-database-yezez9

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 sequencing reads, and genome assemblies for bioinformatics and genomics research.

Core Features & Use Cases

  • Data Retrieval: Fetch sequences, FASTQ files, and genome assemblies by accession number.
  • Metadata Search: Query studies, samples, and experiments using ENA's advanced search API.
  • Taxonomy Lookup: Retrieve taxonomic information for organisms.
  • Use Case: Analyze gene expression patterns by downloading RNA-seq raw reads for a specific study accession and then processing them with downstream bioinformatics tools.

Quick Start

Retrieve all raw sequencing reads for the ENA 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 FASTQ files from ENA using an accession number?▼

You can retrieve raw sequencing reads and FASTQ files from ENA by providing a specific accession number to query the ENA Portal API, which returns the requested nucleotide sequence data for your bioinformatics pipeline.

Can I search for ENA metadata for studies and experiments programmatically?▼

Yes, you can search for ENA metadata for studies, samples, and experiments programmatically by utilizing the ENA Portal API and Browser API to query and filter records based on your specific research criteria.

How do I get taxonomic information for an organism before downloading nucleotide sequences?▼

You can retrieve taxonomic information for an organism by querying the ENA Taxonomy REST API, which provides the necessary cross-referencing data to validate species before fetching genome assemblies or raw reads.

Does this ENA data retrieval method support fetching genome assemblies via FTP?▼

Yes, this ENA data retrieval method supports fetching genome assemblies via both REST APIs and FTP, allowing you to programmatically download large nucleotide sequence datasets directly into your bioinformatics workflows.

What is the best way to integrate ENA nucleotide sequence retrieval into a genomics pipeline?▼

The best way to integrate ENA nucleotide sequence retrieval into a genomics pipeline is by using the ENA Portal API to programmatically fetch sequences and FASTQ files by accession number for immediate downstream processing.

Are there limitations when using ENA Portal API for bulk raw read retrieval?▼

When using the ENA Portal API for bulk raw read retrieval, you must structure your metadata searches carefully to target specific accessions, as fetching unfiltered nucleotide sequence data may overwhelm your REST API query limits.

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