Which biological data formats are supported?

The skill supports a wide range of formats including FASTQ for raw reads, FASTA for sequences, BAM/CRAM for alignments, and XML/JSON for metadata.

Can I perform complex metadata searches with this skill?

Yes, it utilizes the ENA Portal API to filter by study accession, sample attributes, taxonomy, date ranges, and other metadata fields.

What is the ENA Database skill for Claude Code?

It is a specialized capability that allows Claude to programmatically access the European Nucleotide Archive (ENA) for retrieving genomic data, raw sequencing reads, and associated metadata.

Does the skill manage API rate limits?

Yes, it includes best practices for respecting the ENA API limit of 50 requests per second, including exponential backoff and batching strategies.

How does this skill handle large genomic datasets?

For files larger than 100MB, the skill provides implementation patterns for bulk downloading via FTP or Aspera to ensure performance and reliability.

ENA Bioinformatics Database

Name: ENA Bioinformatics Database
Author: Microck

byMicrock

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Data Science & ML

Interfaces with the European Nucleotide Archive to programmatically retrieve DNA/RNA sequences, raw reads, and genome metadata.

The ENA Database skill enables Claude to interact directly with the European Nucleotide Archive (ENA) via REST APIs and FTP. It streamlines the retrieval of nucleotide sequence data, raw sequencing reads (FASTQ), and comprehensive metadata for studies, samples, and assemblies. This skill is essential for bioinformaticians and researchers who need to automate data collection for genomics pipelines, perform taxonomic lookups, or manage high-throughput sequencing data within their development environment.

Key Features

01Bulk data transfer patterns for FTP and Aspera integration

02Direct retrieval of DNA/RNA sequences in FASTA, FASTQ, and EMBL formats

03Cross-reference searching to link ENA records with external biological databases

04Advanced metadata searching using ENA Portal and Browser APIs

0581 GitHub stars

06Comprehensive taxonomic information queries and lineage tracking

Use Cases

01Searching for and downloading specific genome assemblies by accession or metadata criteria

02Automating the retrieval of raw sequencing reads for bioinformatics analysis pipelines

03Integrating ENA data into genomics research software via standardized REST API patterns

What are Skills?·How to Install

Install with 🐟 Skill.Fish

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

For use in Claude.ai and ChatGPT

Download Skill