ena-database

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

Updated Dec 17, 2025

Search Tags:#bioinformatics #genomics #data retrieval #ena #dna sequencing

Ready to run

npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill ena-database-robotlearning123

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: ena-database
Source: https://github.com/robotlearning123/claude-scientific-skills/tree/main/scientific-skills/ena-database
Command: npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill ena-database-robotlearning123

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides a seamless way to access and integrate data from the European Nucleotide Archive (ENA) into your scientific workflows, enabling you to efficiently retrieve, analyze, and process nucleotide sequences, raw reads, and genome assemblies.

Core Features & Use Cases

ENA Data Access: Retrieve DNA/RNA sequences, raw reads, and genome assemblies from ENA using REST APIs and FTP.
Data Retrieval: Download FASTQ files, genome assemblies, and sequence annotations in various formats.
Taxonomy Queries: Access taxonomic information and integrate with related databases.
Use Case: For a genomics research project, quickly retrieve the latest DNA sequences and associated metadata from ENA and integrate them into your analysis pipeline.

Quick Start

Use the ena-database skill to download a genome assembly for the organism with taxon ID 562.

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 reads and genome assemblies from the European Nucleotide Archive?▼

Retrieve nucleotide sequences, raw reads, and genome assemblies from the European Nucleotide Archive by querying the database through a Python interface that handles ENA REST API and FTP data retrieval and parsing.

Can I download FASTQ files and sequence annotations directly from ENA using Python?▼

Yes, you can download FASTQ files, genome assemblies, and sequence annotations directly from ENA using Python. This Skill facilitates data retrieval and parsing through ENA REST APIs and FTP access.

What is the best way to integrate ENA nucleotide sequence data into a bioinformatics pipeline?▼

The best way to integrate ENA nucleotide sequences into a bioinformatics pipeline is using a Python interface that handles data retrieval, parsing, and integration of sequences, raw reads, and genome assemblies accessed via ENA REST APIs and FTP.

Does the ENA database Skill support taxonomy queries for genomics research?▼

Yes, the ENA database Skill supports taxonomy queries for genomics research, allowing you to access taxonomic information and integrate it with related databases alongside retrieved nucleotide sequences and genome assemblies.

Do I need REST API and FTP access to retrieve DNA sequencing data from ENA?▼

Yes, you need access to ENA REST APIs and FTP to retrieve DNA sequencing data. The Python interface requires these protocols to access and download nucleotide sequences, raw reads, and genome assemblies from the European Nucleotide Archive.

How do I download a genome assembly for a specific taxon ID from ENA?▼

To download a genome assembly for a specific taxon ID from ENA, use the Python interface to query the European Nucleotide Archive via REST APIs and FTP, retrieving and parsing the assembly data for integration into your analysis pipeline.