How does the skill handle ENA API rate limits?

The skill includes best practices for ENA's 50 requests per second limit, including implementation of exponential backoff and batching requests to ensure stable data retrieval.

Can I download raw FASTQ files using this skill?

Yes, the skill provides the necessary API endpoints and download patterns to retrieve raw sequencing reads in FASTQ format, as well as BAM, CRAM, and FASTA files.

What is the ENA Database skill for Claude?

This skill provides specialized instructions and API patterns for Claude to interact with the European Nucleotide Archive, allowing for the programmatic retrieval of genomic data and metadata.

What data formats are supported for metadata retrieval?

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

ENA Bioinformatics Integration

Name: ENA Bioinformatics Integration
Author: Activer007

byActiver007

0•

Data Science & ML

Accesses and retrieves genomic data from the European Nucleotide Archive for bioinformatics research and pipelines.

This skill empowers Claude to interact directly with the European Nucleotide Archive (ENA), a premier global repository for DNA and RNA sequence data. It provides specialized knowledge for querying the ENA Portal and Browser APIs, enabling researchers and developers to programmatically retrieve raw reads (FASTQ), genome assemblies, taxonomic metadata, and functional annotations. Whether you are building automated bioinformatics pipelines, searching for specific studies by metadata, or managing bulk data downloads via FTP, this skill streamlines the process of integrating ENA's massive nucleotide datasets into your coding environment.

Key Features

01Taxonomic information and lineage lookup capabilities

02Support for multiple data formats including FASTQ, FASTA, and XML

03Automated retrieval of raw sequencing reads and genome assemblies

04Advanced metadata querying via ENA Portal API

050 GitHub stars

06Guidance on bulk downloading via FTP and Aspera protocols

Use Cases

01Searching and filtering nucleotide records by specific study or metadata criteria

02Building automated data ingestion pipelines for genomic analysis

03Programmatically fetching sequence annotations and functional data for specific accessions

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