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pur3v4d3r
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ena-database

Retrieve ENA nucleotide sequences, raw reads, and genome assemblies by accession.

6|Updated Dec 30, 2025
Search Tags:#api#bioinformatics#taxonomy#ena#downloads#ftp#dna
One-click install
npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill ena-database-pur3v4d3r
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ena-database
Source: https://github.com/pur3v4d3r/pur3-pkb-codebase/tree/main/.claude/skills/__scientific-skills/ena-database
Command: npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill ena-database-pur3v4d3r

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Access to ENA data has historically been manual, fragmented, and slow for genomics workflows. This skill unifies retrieval of nucleotide sequences, raw reads, assemblies, and metadata via ENA REST APIs and FTP for end-to-end pipelines.

Core Features & Use Cases

  • Programmatic data retrieval: fetch studies, samples, runs, assemblies, and taxonomic information by accession or metadata criteria.
  • Bulk and bulk-like downloads: support for batch queries via the Portal API, Browser API, and FTP/Aspera workflows for large data volumes.
  • Cross-referencing and metadata access: leverage ENA cross-references and taxonomy endpoints for integrated analyses and reproducible pipelines.
  • Use Case: Retrieve all reads for a study PRJNA123456 and download FASTQ files for downstream QC and analysis.

Quick Start

Run a basic lookup to fetch FASTQ files for a given ENA accession using the Portal API or Browser API.

Frequently Asked Questions about ena-database

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

FAQPage Schema
How do I download raw reads and FASTQ files from ENA by accession?▼

To download raw reads and FASTQ files from ENA by accession, you can use the Portal API, Browser API, or FTP retrieval methods. This supports batch queries and bulk-like downloads for large data volumes.

What is the best way to programmatically retrieve nucleotide sequences and genome assemblies from ENA?▼

Programmatic retrieval of nucleotide sequences and genome assemblies from ENA is handled via REST APIs. You can fetch studies, samples, runs, and taxonomic information by accession or metadata criteria for downstream pipelines.

Can I batch download metadata and sequence data for an entire ENA study?▼

Yes, you can batch download metadata and sequence data for an entire ENA study. The skill supports batch queries via the Portal API and FTP/Aspera workflows to handle large data volumes efficiently.

Does the ENA API support cross-referencing taxonomy and related records for genomics pipelines?▼

Yes, the ENA API supports cross-referencing taxonomy and related records. You can leverage ENA cross-references and taxonomy endpoints to retrieve integrated metadata for reproducible genomics analyses.

How is rate limiting handled when accessing ENA data programmatically?▼

Rate limiting is handled natively when accessing ENA data programmatically. The skill manages REST API and FTP retrieval workflows, ensuring stable batch downloads and cross-referencing without hitting access barriers.

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