ena-database

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

Updated Aug 23, 2026

Search Tags:#bioinformatics #genomics #sequence retrieval #ena #nucleotide archive #raw reads

Ready to run

npx skills add https://github.com/Zehong-Wang/Kosmos --skill ena-database-zehong-wang

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: ena-database
Source: https://github.com/Zehong-Wang/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/ena-database
Command: npx skills add https://github.com/Zehong-Wang/Kosmos --skill ena-database-zehong-wang

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 research.

Core Features & Use Cases

Data Retrieval: Fetch nucleotide sequences, raw sequencing reads (FASTQ), and genome assemblies by accession number.
Metadata Search: Query ENA for studies, samples, and experiments using various metadata criteria.
API Access: Utilizes ENA's REST APIs for flexible data querying and retrieval.
Use Case: Retrieve all raw sequencing reads (FASTQ files) associated with a specific study accession number for downstream analysis in a genomics pipeline.

Quick Start

Use the ena-database skill to retrieve all raw sequencing reads for 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 from ENA using an accession number?▼

To retrieve raw sequencing reads from ENA, query the REST API or FTP using a specific accession number to download associated FASTQ files for downstream analysis.

What nucleotide data formats can I download from the European Nucleotide Archive?▼

You can download nucleotide data from the European Nucleotide Archive in XML, JSON, TSV, FASTQ, FASTA, and EMBL formats for bioinformatics pipelines.

Can I query ENA metadata for studies, samples, and experiments programmatically?▼

Yes, you can programmatically query ENA metadata for studies, samples, and experiments using various criteria through its REST API endpoints.

How do I get genome assemblies and nucleotide sequences via the ENA REST API?▼

You get genome assemblies and nucleotide sequences via the ENA REST API by submitting requests with specific accession numbers to fetch the required sequence data.

Are there API rate limits when accessing the European Nucleotide Archive for genomic data?▼

Yes, accessing the European Nucleotide Archive requires handling API rate limits to ensure stable programmatic retrieval of genomic data and raw reads.

Does this ENA sequence retrieval method support fetching FASTQ files for genomics pipelines?▼

Yes, this ENA sequence retrieval method supports fetching FASTQ files and genome assemblies directly for integration into bioinformatics and genomics pipelines.