ena-database

Name: ena-database
Availability: InStock
Author: jaechang-hits

Provides programmatic access to European Nucleotide Archive for genomic data retrieval and analysis.

298|27|Updated Feb 18, 2026

Search Tags:#bioinformatics #genomics #taxonomy #sequence retrieval #ena #assembly #data download

Ready to run

npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill ena-database-jaechang-hits

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: ena-database
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/ena-database
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill ena-database-jaechang-hits

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to the European Nucleotide Archive (ENA), enabling users to search for and retrieve genomic sequences, raw reads, assemblies, and annotations without manual web browsing.

Core Features & Use Cases

Search genomic data: Find studies, samples, runs, and assemblies using ENA's query syntax.
Download files: Retrieve raw sequencing reads (FASTQ) and genome assemblies.
Retrieve sequences: Fetch nucleotide sequences in FASTA or EMBL format by accession.
Taxonomy queries: Explore organism lineage and find species information.
Cross-referencing: Link ENA records with external databases like UniProt and PDB.
Use Case: A researcher needs to find all RNA-Seq studies for Homo sapiens published in 2023 and download the FASTQ files for a specific study.

Quick Start

Search for human RNA-seq studies and print their accessions and titles.

Frequently Asked Questions about ena-database

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

FAQPage Schema

How do I download raw sequencing reads and genome assemblies from the European Nucleotide Archive?▼

You can download raw sequencing reads in FASTQ format and genome assemblies from the European Nucleotide Archive programmatically by searching for specific studies, samples, or runs using ENA's query syntax to retrieve the desired files.

Can I fetch nucleotide sequences in FASTA format using an accession number?▼

Yes, you can fetch nucleotide sequences in FASTA or EMBL format by providing a specific accession number, allowing direct retrieval of sequence data from the ENA database without manual web browsing.

How do I search for RNA-Seq studies for a specific organism published in a certain year?▼

You can search for RNA-Seq studies for specific organisms using ENA's query syntax to filter studies, samples, and runs by organism and publication year, returning matching accessions and titles.

Does ENA data retrieval support cross-referencing records with external databases like UniProt and PDB?▼

Yes, ENA data retrieval supports cross-referencing records with external databases like UniProt and PDB, enabling you to link genomic sequences and annotations to related protein structures and functional data.

Can I query taxonomy and organism lineage information through the European Nucleotide Archive?▼

Yes, you can explore organism lineage and find species information through taxonomy queries, allowing you to retrieve detailed taxonomic classifications for organisms stored in the ENA database.

Do I need the requests library to programmatically access ENA genomic data?▼

Yes, the requests library is required as a dependency to programmatically access the European Nucleotide Archive, enabling you to search for genomic data, retrieve sequences, and download files via Python scripts.