Are there rate limits for the ENA API?

The ENA APIs generally have a rate limit of 50 requests per second. This skill includes best practices for handling rate limits and implementing exponential backoff.

Does this skill support bulk downloads?

Yes, it provides guidance for using the Portal API for metadata and explains how to utilize FTP or Aspera for high-speed bulk data transfers.

Can I search for data using metadata instead of accession numbers?

Absolutely. You can perform complex queries using the ENA Portal API to filter results by organism, date range, study type, and various other metadata fields.

What types of data can I retrieve from ENA using this skill?

You can access a wide range of data including studies, samples, raw reads (FASTQ), genome assemblies (FASTA), and detailed taxonomic information.

ENA Genomics Data Access

Name: ENA Genomics Data Access
Author: jimmc414

byjimmc414

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324

Data Science & ML

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

About

This skill enables Claude to interact with the European Nucleotide Archive (ENA), a primary global repository for nucleotide sequencing data. It provides specialized guidance for querying the ENA Portal and Browser APIs to retrieve DNA/RNA sequences, raw sequencing reads (FASTQ), and genome assemblies. Ideal for bioinformaticians and researchers, the skill facilitates searching by metadata, navigating taxonomic records, and integrating public genomics datasets directly into analysis pipelines while adhering to API rate limits and best practices for data citation.

Key Features

Query DNA/RNA sequences and raw reads by accession or metadata criteria
Retrieve genome assemblies and functional annotations via REST APIs
324 GitHub stars
Navigate taxonomic information and cross-reference related databases
Support for multiple formats including FASTQ, FASTA, XML, and JSON
Access hierarchical data structures including studies, samples, experiments, and runs

Use Cases

Searching for and downloading genome assemblies based on specific taxonomic criteria
Extracting metadata and study summaries for large-scale genomic data mining
Automating the retrieval of raw sequencing reads for bioinformatics pipelines

About

Key Features

Query DNA/RNA sequences and raw reads by accession or metadata criteria
Retrieve genome assemblies and functional annotations via REST APIs
324 GitHub stars
Navigate taxonomic information and cross-reference related databases
Support for multiple formats including FASTQ, FASTA, XML, and JSON
Access hierarchical data structures including studies, samples, experiments, and runs

Use Cases

Searching for and downloading genome assemblies based on specific taxonomic criteria
Extracting metadata and study summaries for large-scale genomic data mining
Automating the retrieval of raw sequencing reads for bioinformatics pipelines