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Imad-Oute
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ena-database

Search and download nucleotide sequence data from ENA repositories via REST APIs and FTP.

Updated May 10, 2026
Search Tags:#api#bioinformatics#metadata#genomics#ena#sequence data
One-click install
npx skills add https://github.com/Imad-Oute/ResearchForge --skill ena-database-imad-oute
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ena-database
Source: https://github.com/Imad-Oute/ResearchForge/tree/main/OpenSource-Projects/claude-scientific-skills/scientific-skills/ena-database
Command: npx skills add https://github.com/Imad-Oute/ResearchForge --skill ena-database-imad-oute

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, xml.etree.ElementTree, and includes references (resource) components.

What problem does it solve?

This Skill enables researchers and bioinformaticians to programmatically access and retrieve nucleotide sequence data, metadata, and analysis results from the European Nucleotide Archive via REST APIs and FTP.

Core Features & Use Cases

  • Data Retrieval: Download sequences, raw reads, assemblies, and associated metadata for genomics research.
  • Metadata Search: Query studies, samples, and experiments by accession or metadata criteria for pipeline integration.
  • Use Case: Retrieve all genome assemblies related to a specific organism to generate a comprehensive comparative analysis dataset.

Quick Start

Use the ena-database skill to search for all samples from a study accession and download associated FASTQ files for analysis.

Frequently Asked Questions about ena-database

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

FAQPage Schema
How do I programmatically retrieve nucleotide sequence data and metadata from the ENA database?▼

You can retrieve nucleotide sequence data from the ENA database using REST APIs to search, filter, and download sequences, raw reads, assemblies, and associated metadata across diverse formats for genomics research.

Can I query ENA genome assemblies using a specific study accession?▼

Yes, you can query the ENA database by study accession to retrieve associated samples and experiments, enabling you to download FASTQ files and generate comprehensive comparative analysis datasets for genomics research.

Does the ENA database API support filtering raw reads across different database sections?▼

The ENA database API supports searching and filtering nucleotide sequence data and metadata across diverse database sections, enabling pipelines to target specific raw reads, assemblies, and analysis results effectively.

What do I need to know to use ENA API queries for large-scale genomics projects?▼

Using ENA API queries for large-scale genomics projects requires knowledge of ENA APIs and standard data formats like FASTQ and FASTA to execute complex queries, FTP downloads, and cross-referencing within bioinformatics workflows.

Can I cross-reference external resources when downloading FASTA files from the European Nucleotide Archive?▼

Yes, accessing the European Nucleotide Archive supports cross-referencing external resources when retrieving FASTA files and metadata, which is vital for integrating diverse sequence data into large-scale genomics pipelines.

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