Does this skill help with ENA API rate limits?

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

What types of genomic data can I access with this skill?

You can access a wide range of data including studies, samples, raw reads (FASTQ/CRAM), genome assemblies, annotated sequences, and detailed taxonomic records.

Can I use this for bulk data downloads?

The skill provides patterns for high-speed bulk downloads using FTP, Aspera, and the enaBrowserTools command-line utility for datasets exceeding 100MB.

What metadata formats are supported?

The skill supports metadata retrieval in XML (native ENA format), JSON (via Portal API), and TSV/CSV for tabulated summaries.

Is this suitable for production bioinformatics pipelines?

Yes, it is designed to help Claude generate robust code for data retrieval, handling pagination, status codes, and proper XML/JSON parsing for production environments.

ENA Database Access

Name: ENA Database Access
Author: Sologa

bySologa

0•

Data Science & ML

Retrieves nucleotide sequences, raw sequencing reads, and metadata from the European Nucleotide Archive for genomics research.

The ena-database skill provides Claude with the specialized capability to interact with the European Nucleotide Archive (ENA), a major global repository for nucleotide sequences and associated metadata. It facilitates the programmatic retrieval of DNA/RNA sequences, raw sequencing reads (FASTQ), and genome assemblies using REST APIs and FTP protocols. This skill is particularly useful for bioinformaticians and researchers who need to automate data collection, perform complex metadata queries, or integrate public genomic datasets directly into their analysis pipelines with precision and adherence to best practices.

Key Features

010 GitHub stars

02Programmatic access to ENA Portal and Browser REST APIs

03Retrieval of raw sequencing reads, experiments, and runs

04Support for genome, transcriptome, and metagenome assemblies

05Taxonomic lineage and organism metadata lookups

06Guidance for bulk data transfers via FTP and Aspera

Use Cases

01Querying taxonomic information and related assembly metadata for specific organisms

02Automating the download of FASTQ files for a specific list of study accessions

03Building automated bioinformatics pipelines that require real-time ENA data integration

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add sologa/codex-pipeline ena-database

For use in Claude.ai and ChatGPT

Download Skill