db-ena

Name: db-ena
Availability: InStock
Author: biomaps-infra

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

Updated Mar 13, 2026

Search Tags:#api #data access #bioinformatics #genomics #sequence retrieval #ena #nucleotide archive

Ready to run

npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-ena

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: db-ena
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-ena
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-ena

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 and genomics pipelines.

Core Features & Use Cases

Data Retrieval: Access nucleotide sequences, raw reads (FASTQ), and genome assemblies by accession number.
Metadata Search: Query studies, samples, and experiments using metadata criteria.
API Integration: Supports ENA Portal API, Browser API, and Taxonomy REST API for flexible data access.
Use Case: Retrieve all raw sequencing reads (FASTQ files) for a specific ENA run accession to analyze microbial genomes.

Quick Start

Use the db-ena skill to find all samples associated with the ENA study accession PRJEB1234.

Frequently Asked Questions about db-ena

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?▼

You can retrieve raw sequencing reads and genome assemblies from the European Nucleotide Archive by querying with specific accession numbers via the Portal API and Browser API. This returns data in formats including FASTQ, FASTA, BAM, and CRAM for bioinformatics pipelines.

Can I search for ENA studies and samples using taxonomic information and metadata?▼

Yes, searching ENA studies and samples using taxonomic information and metadata is supported through the Taxonomy REST API. You can query experiments using metadata criteria to find all samples associated with a specific study accession like PRJEB1234.

What data formats are supported when accessing nucleotide sequences through the ENA Portal API?▼

Accessing nucleotide sequences through the ENA Portal API supports data formats including JSON, TSV, XML, FASTQ, FASTA, BAM, and CRAM. This allows direct integration of retrieved DNA and RNA sequences into bioinformatics workflows.

What is the best way to programmatically access nucleotide sequences for a genomics pipeline?▼

The best way to programmatically access nucleotide sequences for genomics pipelines is using REST APIs and FTP. This enables automated retrieval of raw reads and genome assemblies by accession number, handling metadata searches for bioinformatics analysis.

Does this data access method require specific dependencies to retrieve FASTQ files?▼

No specific dependencies are required to retrieve FASTQ files, as access is handled programmatically through REST APIs and FTP. You can directly query run accessions to download raw sequencing reads without needing additional software libraries.