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LogauaEngstrom
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ena-database

Access ENA genomics data via REST APIs and FTP/Aspera.

18|1|Updated Dec 27, 2025
Search Tags:#api#bioinformatics#genomics#taxonomy#ena#bulk-download#data-retrieval
One-click install
npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill ena-database-logauaengstrom
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ena-database
Source: https://github.com/LogauaEngstrom/claude-scientific-skills/tree/main/scientific-skills/ena-database
Command: npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill ena-database-logauaengstrom

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ENA hosts a comprehensive public nucleotide data archive; without automation, researchers struggle to locate, retrieve, and download sequences, reads, and assemblies across multiple APIs.

Core Features & Use Cases

  • Centralized programmatic access to ENA Portal API, ENA Browser API, TAXON API, and Cross-Reference services.
  • Retrieve data by accession, search by metadata, and bulk download data via FTP/Aspera for genomics pipelines.
  • Supports multiple data formats (XML, JSON, TSV/CSV, FASTA/FASTQ) and bulk download tooling.
  • Use Case: Retrieve all reads for a study and download FASTQ files for downstream analysis.

Quick Start

Query the ENA Portal API to retrieve all samples for a given study and download their FASTQ files.

Frequently Asked Questions about ena-database

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

FAQPage Schema
How do I retrieve sequences from ENA using an accession number?▼

Accession-based retrieval uses the ENA Portal API or Browser API to fetch sequences and associated metadata in XML, JSON, TSV, or FASTA formats. This provides direct programmatic access for integrating public nucleotide data into genomics pipelines.

What is the best way to bulk download FASTQ files for a study?▼

Bulk download FASTQ reads for an entire study via FTP or Aspera protocols. This method handles large-scale data retrieval efficiently, providing the raw sequencing files needed for downstream genomics workflows.

Can I search the ENA database by metadata rather than accession?▼

Search ENA by metadata using the Portal API and TAXON API to locate samples matching specific taxonomic or experimental criteria. This filters public nucleotide archives to find relevant sequences before downloading any data files.

What data formats are supported when retrieving genomics data from the ENA API?▼

ENA APIs support XML, JSON, TSV, CSV, FASTA, and FASTQ data formats for sequence retrieval. This format flexibility ensures compatibility with diverse bioinformatics pipelines for both metadata parsing and raw read processing.

Does the ENA API have rate limits I need to handle for automated data retrieval?▼

ENA APIs enforce rate limits that require automated retry logic and error handling during data retrieval. Implementing these strategies ensures robust pipeline integration when fetching large volumes of genomics data without connection failures.

How do I get taxonomic information for samples retrieved from ENA?▼

Retrieve taxonomic information for ENA samples by querying the dedicated TAXON API and Cross-Reference services. This provides detailed taxonomy data and external database mappings to support annotation retrieval in genomics workflows.

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