What is the ENA Database skill for Claude Code?

It is a specialized capability that enables Claude to interact with the European Nucleotide Archive to search, retrieve, and manage genomic data and metadata.

Can I search for data using taxonomic names?

Absolutely. The skill supports searching for assemblies and samples using taxonomic criteria and organism names via the ENA Taxonomy REST API.

Which genomic file formats are supported?

The skill supports various formats including FASTQ (raw reads), FASTA (assembled sequences), BAM/CRAM (aligned reads), and XML/JSON for metadata.

Can I use this skill for bulk data downloads?

Yes, while it uses REST APIs for queries, it also provides implementation patterns for bulk downloads via FTP and Aspera for large datasets.

Does it handle API rate limiting?

Yes, the skill includes best practices for handling the ENA's 50 requests per second limit, including exponential backoff and batching strategies.

European Nucleotide Archive (ENA) Access

Name: European Nucleotide Archive (ENA) Access
Author: Activer007

byActiver007

0•

Data Science & ML

Accesses and retrieves genomic data, nucleotide sequences, and metadata from the European Nucleotide Archive (ENA) via REST APIs and FTP.

This skill provides Claude with specialized capabilities to interact with the European Nucleotide Archive (ENA), allowing for programmatic retrieval of DNA/RNA sequences, raw sequencing reads, and genome assemblies. It streamlines bioinformatics workflows by facilitating metadata searches across studies and samples, taxonomic lookups, and the integration of diverse file formats like FASTQ and FASTA into analysis pipelines. Whether searching for specific accessions or performing bulk downloads via API or FTP, this skill serves as a comprehensive bridge between AI-driven development and one of the world's primary nucleotide sequence repositories.

Key Features

01Advanced metadata searching across ENA studies, samples, and experiments

02Guidance for high-speed bulk data transfers using FTP and Aspera

03Taxonomic information retrieval and lineage mapping via the Taxonomy API

04Support for multiple data formats including FASTQ, FASTA, XML, and JSON

050 GitHub stars

06Programmatic retrieval of sequences and raw reads by accession number

Use Cases

01Automating the retrieval of FASTQ files and raw reads for bioinformatics pipelines

02Extracting genome assemblies and functional annotations for comparative genomics

03Searching for all genomic samples and studies associated with specific organisms

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills ena-database

For use in Claude.ai and ChatGPT

Download Skill