Does it support taxonomic queries?

Yes, the skill includes support for the ENA Taxonomy REST API to query lineage, rank, and related taxonomic data for organisms.

Are there rate limits for ENA API access?

Yes, ENA APIs generally limit requests to 50 per second. This skill includes best practices for implementing exponential backoff and batching to stay within these limits.

What data formats are supported?

The skill facilitates retrieval in multiple formats including XML, JSON, and TSV for metadata, and FASTQ, FASTA, CRAM, and EMBL flat files for sequence data.

Can this skill download large sequencing files?

Yes, it provides guidance and programmatic patterns for using ENA's FTP and Aspera services for high-speed bulk transfers of large data files like FASTQ or BAM/CRAM.

ENA Database Integration

Name: ENA Database Integration
Author: Microck

byMicrock

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データサイエンスとML

Accesses and retrieves nucleotide sequence data, raw reads, and genome assemblies from the European Nucleotide Archive (ENA).

概要

This skill empowers Claude to interact programmatically with the European Nucleotide Archive (ENA), a premier global repository for genetic sequence data. It facilitates complex metadata searches via the Portal API, direct retrieval of raw reads (FASTQ) and annotated sequences (EMBL/FASTA) via the Browser API, and provides implementation patterns for high-speed bulk downloads using FTP or Aspera. Whether you are building a bioinformatics pipeline, conducting taxonomic research, or needing specific genome assemblies, this skill provides the specific guidance and API patterns required to integrate ENA data seamlessly into your genomics workflow.

主な機能

Advanced metadata searching using ENA Portal API
Access to genome assemblies and functional annotations
Retrieval of raw sequencing reads and FASTQ files
Taxonomic lineage and organism metadata queries
Guidance for high-speed bulk data transfer via FTP and Aspera
89 GitHub stars

ユースケース

Searching for all assemblies associated with specific taxonomic IDs
Building cross-reference searches between ENA and external biological databases
Automating the retrieval of sample datasets for genomics pipelines

概要

主な機能

Advanced metadata searching using ENA Portal API
Access to genome assemblies and functional annotations
Retrieval of raw sequencing reads and FASTQ files
Taxonomic lineage and organism metadata queries
Guidance for high-speed bulk data transfer via FTP and Aspera
89 GitHub stars

ユースケース

Searching for all assemblies associated with specific taxonomic IDs
Building cross-reference searches between ENA and external biological databases
Automating the retrieval of sample datasets for genomics pipelines