Does this skill support bulk downloads?

Yes, it provides documentation and patterns for using FTP and Aspera for high-speed, large-scale data transfers beyond simple API calls.

Are there rate limits for ENA API requests?

Yes, ENA APIs generally have a rate limit of 50 requests per second. The skill includes best practices for handling rate limiting and performance.

What data can I access through this ENA skill?

You can access DNA/RNA sequences, raw reads (FASTQ), genome assemblies, study metadata, and taxonomic records directly from the European Nucleotide Archive.

Can I search for data by organism name?

Yes, you can query taxonomic information and find assemblies or sequences related to specific organisms using the integrated Taxonomy API functionality.

Which APIs are used by this skill?

The skill utilizes the ENA Portal API for advanced searches and the Browser API for direct record and metadata retrieval.

European Nucleotide Archive Integration

Name: European Nucleotide Archive Integration
Author: Microck

byMicrock

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Data Science & ML

Accesses and retrieves genomic data, including DNA/RNA sequences and raw reads, from the European Nucleotide Archive (ENA) via REST APIs and FTP.

About

This skill empowers Claude to interact with the European Nucleotide Archive (ENA), a premier global repository for nucleotide sequence data. It provides streamlined access to diverse data types including raw sequencing reads (FASTQ), genome assemblies, and annotated sequences. By leveraging ENA's Portal and Browser APIs, the skill enables advanced metadata searching, taxonomic lineage queries, and bulk data retrieval, making it an essential resource for bioinformaticians and researchers building automated genomic analysis pipelines.

Key Features

Comprehensive retrieval of DNA/RNA sequences and raw sequencing reads (FASTQ/BAM/CRAM)
Integration guidance for bulk downloads via FTP and high-speed Aspera transfers
81 GitHub stars
Advanced metadata search using the ENA Portal API for studies, samples, and runs
Taxonomic information querying and lineage retrieval for organisms
Support for multiple data formats including XML, JSON, FASTA, and EMBL flat files

Use Cases

Automating the retrieval of sequencing data for specific studies by project accession
Finding all genome assemblies and related functional annotations for a specific taxon
Building bioinformatics pipelines that require programmatic metadata from the ENA database

About

Key Features

Comprehensive retrieval of DNA/RNA sequences and raw sequencing reads (FASTQ/BAM/CRAM)
Integration guidance for bulk downloads via FTP and high-speed Aspera transfers
81 GitHub stars
Advanced metadata search using the ENA Portal API for studies, samples, and runs
Taxonomic information querying and lineage retrieval for organisms
Support for multiple data formats including XML, JSON, FASTA, and EMBL flat files

Use Cases

Automating the retrieval of sequencing data for specific studies by project accession
Finding all genome assemblies and related functional annotations for a specific taxon
Building bioinformatics pipelines that require programmatic metadata from the ENA database