Can I perform bulk downloads with this skill?

Yes, the skill provides implementation patterns for bulk downloading datasets via FTP or Aspera, which is recommended for high-speed transfer of large genomic files.

How does this skill help with ENA Portal API queries?

It provides standardized patterns for constructing complex queries to filter data by study accession, project ID, sample metadata, and specific data types.

What data formats does the ENA Database skill support?

The skill supports various formats including FASTQ for raw reads, FASTA for sequences, EMBL flat files for annotations, and metadata in XML, JSON, or TSV formats.

Does it handle ENA API rate limits?

Yes, it provides guidance on implementing exponential backoff to respect the ENA API limit of 50 requests per second, ensuring stable data retrieval.

Can I search for data by taxonomy?

Absolutely. You can query taxonomic information including lineage and rank, and perform searches for assemblies or samples based on specific organism names or taxonomic IDs.

ENA Database Access

Name: ENA Database Access
Author: Activer007

byActiver007

Data Science & ML

Simplifies retrieval of nucleotide sequences, raw reads, and genome assemblies from the European Nucleotide Archive for bioinformatics pipelines.

About

The ENA Database skill empowers researchers and bioinformaticians to programmatically interact with the European Nucleotide Archive (ENA) directly through Claude. It provides a streamlined interface for querying complex metadata, accessing taxonomy records, and downloading various genomic data formats like FASTQ, FASTA, and EMBL flat files. Whether you are automating large-scale dataset retrieval via FTP or performing targeted searches for specific study accessions, this skill handles the complexities of ENA's multi-layered REST APIs, rate limiting, and data hierarchy, making it an essential tool for accelerating genomics research and pipeline integration.

Key Features

Advanced metadata search and filtering via ENA Portal API
Comprehensive taxonomic lineage and rank querying
Automated rate limiting and exponential backoff management
0 GitHub stars
Direct sequence and assembly retrieval by accession number
Support for multiple formats including FASTQ, FASTA, and XML

Use Cases

Integrating ENA cross-references into existing genomic analysis pipelines
Automating the download of raw sequencing reads for new bioinformatics projects
Searching and filtering genome assemblies by organism or metadata criteria

About

Key Features

Advanced metadata search and filtering via ENA Portal API
Comprehensive taxonomic lineage and rank querying
Automated rate limiting and exponential backoff management
0 GitHub stars
Direct sequence and assembly retrieval by accession number
Support for multiple formats including FASTQ, FASTA, and XML

Use Cases

Integrating ENA cross-references into existing genomic analysis pipelines
Automating the download of raw sequencing reads for new bioinformatics projects
Searching and filtering genome assemblies by organism or metadata criteria