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LeonChaoX
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ena-database

Retrieve nucleotide sequences and metadata from European Nucleotide Archive APIs.

783|65|Updated Feb 27, 2026
Search Tags:#genomics#taxonomy#ena#api search#bioinformatics pipeline#fastq retrieval#sequence assemblies
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill ena-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ena-database
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/ena-database
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill ena-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill solves the problem of manually searching and downloading nucleotide sequence data by accession or metadata from the European Nucleotide Archive, replacing slow, error-prone data retrieval with structured API-driven downloads for downstream genomics analysis.

Core Features & Use Cases

  • Accession-based retrieval: Pull nucleotide sequences and related records such as runs (raw reads), assemblies, and annotations using ENA Browser API endpoints.
  • Metadata search at scale: Use ENA Portal API advanced queries to find samples, studies, read runs, and assemblies by taxonomy, fields, and date constraints.
  • Bulk download workflows: Support efficient acquisition of FASTQ and assemblies via FTP/Aspera patterns and file-report style metadata needed for pipeline execution.
  • Cross-reference and taxonomy lookup: Retrieve links to external databases and taxonomic lineage information to enrich analysis and improve reproducibility.

Quick Start

Ask an AI agent to retrieve FASTQ download URLs for run accession ERR123456 from ENA and return them in a pipeline-ready list.

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 FASTQ files from ENA using an accession number?▼

To retrieve raw sequencing reads and assemblies without manual browsing, this Skill uses ENA Portal and Browser APIs for structured search. It supports REST endpoints, multiple output formats, and accession-based retrieval to fetch nucleotide records for genomics pipelines.

How do I search for ENA nucleotide records by taxonomy and metadata at scale?▼

When building bioinformatics pipelines, this Skill provides rate-limit aware access and pagination-friendly querying to retrieve FASTQ files and assemblies. It supports FTP and Aspera download patterns for efficient bulk acquisition of nucleotide sequence data.

Can I retrieve taxonomic lineage information and external database cross-references from ENA?▼

This Skill is designed for bioinformatics pipelines requiring structured, API-driven downloads from the European Nucleotide Archive. It replaces slow, error-prone manual browsing with programmatic retrieval of DNA/RNA sequences and associated metadata.

What is the best way to automate bulk download of genome assemblies from the European Nucleotide Archive?▼

The best way to automate bulk assembly downloads is using the ENA Portal API's file-report style metadata to retrieve FTP and Aspera download patterns. This Skill orchestrates structured bulk retrieval of genome and transcriptome assemblies for downstream analysis.

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