Can I search for sequences by organism?

Yes, you can query taxonomic information and search for assemblies or samples using the ENA Taxonomy REST API and Portal API's tax_tree queries.

What formats are supported for metadata?

Metadata can be retrieved in XML (native ENA Browser API format), JSON (via Portal API), and TSV/CSV for tabulated summaries.

What types of data can I retrieve using this skill?

You can access DNA/RNA sequences, raw sequencing reads (FASTQ/CRAM), genome assemblies, study metadata, and taxonomic records.

Does this skill support bulk downloads?

Yes, it provides implementation patterns for using the ENA Portal API to identify accessions and then downloading via FTP or Aspera for high-speed transfers.

How does the skill handle ENA API rate limits?

It incorporates best practices for rate limiting, recommending exponential backoff and staying within the 50 requests per second limit to avoid HTTP 429 errors.

ENA Bioinformatics Database

Name: ENA Bioinformatics Database
Author: Microck

byMicrock

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Ciencia de Datos y ML

Accesses and retrieves genomic data from the European Nucleotide Archive (ENA) via REST APIs and FTP for bioinformatics pipelines.

Acerca de

This skill enables Claude to interact effectively with the European Nucleotide Archive (ENA), a premier global repository for nucleotide sequence data. It provides structured guidance for querying metadata, retrieving raw sequencing reads (FASTQ), downloading genome assemblies, and accessing functional annotations. By integrating ENA's Portal and Browser APIs, the skill facilitates the automation of data discovery and retrieval for genomics, transcriptomics, and metagenomics research, ensuring high-speed transfers and adherence to rate-limiting best practices for scientific workflows.

Características Principales

Advanced metadata searching using ENA Portal API
Taxonomic information and lineage querying via REST API
Direct retrieval of DNA/RNA sequences and raw reads (FASTQ/CRAM)
Guidance on bulk data transfer via FTP and Aspera tools
Support for multiple data formats including XML, JSON, and TSV
81 GitHub stars

Casos de Uso

Searching for genome assemblies based on organism taxonomic criteria
Automating the retrieval of sequencing data for specific studies or projects
Integrating ENA data access into automated bioinformatics analysis pipelines

Acerca de

Características Principales

Advanced metadata searching using ENA Portal API
Taxonomic information and lineage querying via REST API
Direct retrieval of DNA/RNA sequences and raw reads (FASTQ/CRAM)
Guidance on bulk data transfer via FTP and Aspera tools
Support for multiple data formats including XML, JSON, and TSV
81 GitHub stars

Casos de Uso

Searching for genome assemblies based on organism taxonomic criteria
Automating the retrieval of sequencing data for specific studies or projects
Integrating ENA data access into automated bioinformatics analysis pipelines