Does this skill handle ENA API rate limiting?

Yes, it provides best practices for managing ENA's limit of 50 requests per second, including implementation patterns for exponential backoff and batching.

In what formats can I download ENA metadata?

Metadata can be retrieved in XML (native), JSON (via Portal API), or tabulated TSV/CSV summaries for easier parsing in data pipelines.

How does the skill handle large file downloads?

It provides guidance on using high-speed transfer methods like FTP, Aspera, and the enaBrowserTools command-line utility for datasets exceeding 100MB.

Which ENA APIs are supported by this skill?

The skill supports the ENA Portal API for advanced searches, the Browser API for record retrieval, the Taxonomy REST API, and the Cross Reference Service.

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

You can access a wide range of data including DNA/RNA sequences, raw sequencing reads (FASTQ), genome assemblies, and associated metadata for studies and samples.

ENA Database Integration

Name: ENA Database Integration
Author: K-Dense-AI

byK-Dense-AI

•

2,188

Data Science & ML

Access and retrieve comprehensive nucleotide sequence data and metadata from the European Nucleotide Archive (ENA) for bioinformatics pipelines.

About

The ENA Database skill empowers Claude to interact programmatically with the European Nucleotide Archive, providing direct access to DNA/RNA sequences, raw reads, and genome assemblies. It streamlines the process of querying ENA's complex hierarchical metadata, navigating REST API rate limits, and implementing best practices for retrieving large-scale datasets. Whether you are searching for specific studies, downloading FASTQ files, or fetching taxonomic lineages, this skill provides the implementation patterns and API references required for robust genomic data management and research automation.

Key Features

2,188 GitHub stars
Multi-API support including ENA Portal, Browser, and Taxonomy REST APIs
Automated metadata search and cross-reference lookups
Optimized retrieval for FASTQ, FASTA, BAM, and CRAM formats
Hierarchical data navigation across Studies, Samples, and Runs
Bulk download guidance via FTP, Aspera, and enaBrowserTools

Use Cases

Searching for genome assemblies based on specific organism taxonomic criteria
Integrating ENA metadata harvesting into automated bioinformatics analysis pipelines
Automating the retrieval of raw sequencing reads for specific research accessions

About

Key Features

2,188 GitHub stars
Multi-API support including ENA Portal, Browser, and Taxonomy REST APIs
Automated metadata search and cross-reference lookups
Optimized retrieval for FASTQ, FASTA, BAM, and CRAM formats
Hierarchical data navigation across Studies, Samples, and Runs
Bulk download guidance via FTP, Aspera, and enaBrowserTools

Use Cases

Searching for genome assemblies based on specific organism taxonomic criteria
Integrating ENA metadata harvesting into automated bioinformatics analysis pipelines
Automating the retrieval of raw sequencing reads for specific research accessions