How does this skill handle rate limiting?

It includes guidance on implementing exponential backoff and batching requests to stay within the ENA API limit of 50 requests per second.

Can I download large FASTQ files using this skill?

Yes, the skill provides patterns for identifying file URLs and utilizing FTP or Aspera for high-speed bulk data transfers.

Does it support metadata searches?

Yes, it utilizes the ENA Portal API for advanced searches across studies, samples, and experiments using complex metadata criteria.

What types of genomic data are supported?

The skill supports raw reads, genome/transcriptome assemblies, annotated sequences, and taxonomic records.

European Nucleotide Archive (ENA) Access

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

byActiver007

0•

Data Science & ML

Connects Claude to the European Nucleotide Archive (ENA) for retrieving genomic sequences, raw reads, and metadata.

This skill empowers Claude to interact programmatically with the European Nucleotide Archive (ENA), a leading global repository for nucleotide sequence data. It allows for the retrieval of DNA and RNA sequences, raw sequencing reads (FASTQ), and genome assemblies via REST APIs or FTP. Whether you are performing taxonomic lookups, searching for specific studies, or automating the ingestion of datasets into bioinformatics pipelines, this skill provides the structure and guidance needed to handle high-volume genomic data and metadata efficiently.

Key Features

01Support for multiple data formats including FASTQ, FASTA, XML, and JSON

02Advanced search capabilities for studies, samples, experiments, and runs

030 GitHub stars

04Guidance on high-speed data transfer via FTP and Aspera for bulk datasets

05Programmatic access to ENA Portal and Browser APIs for metadata and record retrieval

06Taxonomy integration for querying organism lineage and rank

Use Cases

01Integrating public genomic data into automated bioinformatics analysis pipelines

02Automating the retrieval of raw sequencing reads (FASTQ) for specific study accessions

03Filtering and searching for genome assemblies based on taxonomic criteria

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