skills.rest
Org-GAgent
Org-GAgentOFFICIAL
Explore all skills by this author →
GitHub

ena-database

Query ENA studies, samples, runs, and assemblies via Portal and taxonomy APIs.

Updated Aug 23, 2026
Search Tags:#api#bioinformatics#taxonomy#ena#bulk-download#data-retrieval
One-click install
npx skills add https://github.com/Org-GAgent/result-interpreter --skill ena-database-org-gagent
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ena-database
Source: https://github.com/Org-GAgent/result-interpreter/tree/main/.skills/scientific-skills/ena-database
Command: npx skills add https://github.com/Org-GAgent/result-interpreter --skill ena-database-org-gagent

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

The ENA database skill enables programmatic access to nucleotide sequence data and associated metadata through ENA Portal API, Browser API, and FTP, allowing users to retrieve studies, samples, reads, assemblies, and taxonomic information for genomics pipelines.

Core Features & Use Cases

  • Programmatic querying of ENA data across studies, samples, experiments, reads, assemblies, sequences, and analyses
  • Cross-reference services and bulk data download via FTP/Aspera for large datasets
  • Integrate ENA data into bioinformatics workflows for analysis, annotation, and reporting

Quick Start

Query ENA data via API or FTP to pull records for a given study and accessions.

Frequently Asked Questions about ena-database

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

FAQPage Schema
How do I query ENA data programmatically for bioinformatics workflows?▼

You can query ENA data programmatically using Portal, Browser, and taxonomy APIs to retrieve studies, samples, runs, assemblies, and sequences. Results are available in JSON, TSV, XML, and sequence formats for integration into bioinformatics pipelines.

What is the best way to bulk download large nucleotide sequence datasets from ENA?▼

Bulk download of large ENA datasets is supported via FTP and Aspera protocols. The Skill provides guidance for retrieving large nucleotide sequence datasets and associated metadata while applying rate-limiting awareness and error handling.

Can I cross-reference external resources when retrieving ENA sequence data?▼

Yes, cross-reference services are supported across ENA endpoints when retrieving sequence data. You can cross-reference external resources to link studies, samples, and assemblies with related database records during data retrieval.

Does the ENA API support taxonomic querying for genomics pipelines?▼

The ENA taxonomy API supports taxonomic querying for genomics pipelines. You can retrieve taxonomic information alongside studies, samples, and reads to annotate sequences and enrich bioinformatics analysis workflows.

What data formats are available when querying ENA records via the API?▼

Querying ENA records via the API returns data in JSON, TSV, XML, and sequence formats. Format selection depends on your bioinformatics workflow requirements for metadata parsing and nucleotide sequence data retrieval.

What are the limitations when accessing ENA data through Portal and Browser APIs?▼

Limitations include API rate-limiting constraints that require awareness during programmatic access. The Skill provides error handling guidance for Portal and Browser API queries to manage retrieval failures and ensure stable data access.

Related Skills

Explore More Data & Analytics Skills→
sanand0sanand0
8

ena-database

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

Community
Intermediate
sagunkayasthasagunkayastha

ena-database

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

Community
Advanced
LogauaEngstromLogauaEngstrom
18

ena-database

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

Community
Advanced
AvaTar-ArTsAvaTar-ArTs

tooluniverse-sequence-retrieval

Retrieve biological sequences from NCBI and ENA into FASTA or GenBank formats.

Community
Advanced