alterlab-ena

Retrieve nucleotide sequence data and metadata from ENA via REST APIs.

58|9|Updated Mar 16, 2026

Search Tags:#api #bioinformatics #genomics #taxonomy #ena #data-retrieval

Ready to run

npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-ena

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: alterlab-ena
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/databases/alterlab-ena
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-ena

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ENA is a comprehensive public repository for nucleotide sequence data and associated metadata. Access and query DNA/RNA sequences, raw reads, genome assemblies, and functional data through REST APIs and FTP for genomics and bioinformatics pipelines.

Core Features & Use Cases

Data types and organization: Studies/Projects, Samples, Raw Reads, Assemblies, Sequences, Analyses, Taxonomy Records.
Programmatic access: ENA Portal API, ENA Browser API, ENA Taxonomy REST API, Cross-Reference Service, CRAM Reference Registry.
Data retrieval formats and methods: metadata in JSON/TSV/XML, sequence data in FASTA/FASTQ/EMBL, downloads via FTP/Aspera or enaBrowserTools.
Common use cases: search samples by study, retrieve runs, download assemblies, cross-reference records, bulk data access.

Quick Start

Use the Portal API to search for samples by study_accession and retrieve results in JSON.

Frequently Asked Questions about alterlab-ena

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

FAQPage Schema

How do I retrieve nucleotide sequence data from ENA for genomics workflows?▼

To retrieve nucleotide sequence data from ENA, you can use the Portal API or Browser API to search for studies, samples, runs, and assemblies, retrieving results in formats like JSON, TSV, or XML.

What formats are available when downloading raw reads and genome assemblies from ENA?▼

When downloading raw reads and genome assemblies from ENA, available sequence data formats include FASTA, FASTQ, and EMBL. Metadata can be retrieved in JSON, TSV, or XML formats via FTP or Aspera.

Can I cross-reference taxonomy records and samples using the ENA API?▼

Yes, you can cross-reference taxonomy records and samples using the ENA Taxonomy REST API and the Cross-Reference Service to link studies, samples, and runs across different database records.

What is the best way to bulk download genomics data from ENA?▼

For bulk genomics data access from ENA, use FTP or Aspera for large file transfers. The enaBrowserTools provides command-line utilities to automate and structure bulk downloads reliably.

Are there rate-limiting guidelines for programmatic ENA API access?▼

Yes, programmatic ENA API access includes rate-limiting guidance to ensure reliable integration. Structured querying patterns are provided to maintain consistent API access without exceeding request thresholds.

How do I search for sequencing runs by study accession using the ENA Portal API?▼

You can search for sequencing runs by study accession using the ENA Portal API by applying a structured query with the study_accession parameter, returning matching run metadata in your specified format.