Can this skill download large sequencing files?

Yes, while small records are retrieved via API, the skill provides guidance for bulk downloads of large datasets (over 100MB) using FTP or Aspera protocols.

What is the European Nucleotide Archive (ENA)?

The ENA is a comprehensive public repository for nucleotide sequence data, providing access to raw reads, genome assemblies, and functional annotations managed by EMBL-EBI.

How does the skill handle API rate limits?

The skill follows ENA's performance guidelines, implementing exponential backoff and batching strategies to remain within the limit of 50 requests per second.

Does it support complex metadata queries?

Yes, it utilizes the ENA Portal API which allows for advanced filtering by study accession, sample attributes, date ranges, and taxonomic lineages.

ENA Bioinformatics Database

Name: ENA Bioinformatics Database
Author: BbgnsurfTech

byBbgnsurfTech

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Ciencia de Datos y ML

Accesses and retrieves nucleotide sequences, raw reads, and genomic metadata from the European Nucleotide Archive (ENA).

Acerca de

This skill enables researchers and bioinformaticians to programmatically interface with the European Nucleotide Archive (ENA) to fetch DNA/RNA sequences, genome assemblies, and associated metadata. It facilitates complex queries via the ENA Portal and Browser APIs, taxonomy lookups, and bulk data retrieval through FTP or Aspera. By providing standardized implementation patterns for bioinformatics pipelines, it helps users automate the collection of archival biological data for large-scale genomic analysis and sequence annotation tasks.

Características Principales

Integration with high-speed bulk download methods like FTP and Aspera
3 GitHub stars
Advanced metadata search and filtering for studies, samples, and runs
Programmatic access to ENA Portal, Browser, and Taxonomy APIs
Built-in best practices for API rate limiting and error handling
Support for diverse formats including FASTQ, FASTA, XML, and JSON

Casos de Uso

Automating the retrieval of raw sequencing reads (FASTQ) for analysis pipelines
Searching and filtering genomic assemblies by taxonomic criteria or metadata
Accessing functional annotations and cross-references for specific nucleotide accessions

Acerca de

Características Principales

Integration with high-speed bulk download methods like FTP and Aspera
3 GitHub stars
Advanced metadata search and filtering for studies, samples, and runs
Programmatic access to ENA Portal, Browser, and Taxonomy APIs
Built-in best practices for API rate limiting and error handling
Support for diverse formats including FASTQ, FASTA, XML, and JSON

Casos de Uso

Automating the retrieval of raw sequencing reads (FASTQ) for analysis pipelines
Searching and filtering genomic assemblies by taxonomic criteria or metadata
Accessing functional annotations and cross-references for specific nucleotide accessions