skills.rest
Sologa
SologaCOMMUNITY
Explore all skills by this author →
GitHub

ena-database

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

1|Updated Jan 14, 2026
Search Tags:#data access#bioinformatics#genomics#sequence retrieval#ena#nucleotide archive
One-click install
npx skills add https://github.com/Sologa/codex-pipeline --skill ena-database-sologa
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ena-database
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/ena-database
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill ena-database-sologa

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 sequencing reads, and genome assemblies for bioinformatics pipelines.

Core Features & Use Cases

  • Data Retrieval: Fetch sequences, raw reads (FASTQ), and genome assemblies by accession number.
  • Metadata Search: Query ENA for studies, samples, and experiments based on various metadata criteria.
  • Bulk Downloads: Facilitates downloading large datasets via FTP or Aspera.
  • Use Case: Retrieve all raw sequencing reads (FASTQ files) associated with a specific study accession number for downstream analysis.

Quick Start

Use the ena-database skill to find all samples associated with the study accession PRJEB1234.

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 and FASTQ files from ENA using an accession number?▼

To retrieve raw sequencing reads and FASTQ files from ENA, query the database by study accession number using the Portal API. This enables programmatic access to fetch raw sequencing reads and genome assemblies for downstream bioinformatics pipelines.

Can I download bulk genomic data from the European Nucleotide Archive via FTP and Aspera?▼

Yes, you can download bulk genomic data from the European Nucleotide Archive via FTP and Aspera. The Skill facilitates large dataset transfers, supporting comprehensive data querying and access for genomics pipelines.

What is the best way to search ENA metadata for specific studies, samples, and experiments?▼

The best way to search ENA metadata for specific studies, samples, and experiments is using the Browser API and Taxonomy API. These REST APIs support comprehensive data querying based on various metadata criteria.

Does programmatic access to ENA require any specific dependencies or environment setup?▼

Programmatic access to ENA requires no specific dependencies or environment setup. The Skill operates independently to enable data retrieval via REST APIs and FTP/Aspera for bulk transfers in genomics pipelines.

When should I use the ENA Portal API versus the Browser API for nucleotide sequence retrieval?▼

Use the ENA Portal API to fetch nucleotide sequences and genome assemblies by accession number, and the Browser API to query metadata for studies and samples. Both facilitate comprehensive data retrieval for bioinformatics pipelines.

Related Skills

Explore More Education & Research Skills→
ovachieverovachiever
52

ena-database

Retrieve nucleotide sequences and associated data from ENA via REST APIs.

Community
Advanced
tassiovaletassiovale
13

pysam

Automate genomic data processing with pysam for SAM, BAM, CRAM, VCF, BCF, FASTA, and FASTQ files.

Community
Advanced
biomaps-infrabiomaps-infra

db-ena

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

Official
Advanced
AvaTar-ArTsAvaTar-ArTs

tooluniverse-sequence-retrieval

Retrieve DNA, RNA, and protein sequences from NCBI and ENA with accession-based disambiguation.

Community
Intermediate