What is the European Nucleotide Archive (ENA)?

The ENA is a comprehensive public repository for nucleotide sequence data, encompassing raw sequencing reads, genome assemblies, and functional annotations.

How do I search for specific organisms using this skill?

You can use the built-in taxonomy API capabilities to query by taxon ID or organism name to find related assemblies, samples, and study records.

Does this skill handle ENA API rate limiting?

Yes, it includes best practices for managing the ENA's 50 requests per second limit, including implementing exponential backoff and batching requests.

What formats can I retrieve data in?

The skill supports metadata in JSON, XML, and TSV/CSV formats, and sequence data in FASTQ, FASTA, BAM, CRAM, and EMBL flat file formats.

Can I use this skill for bulk sequencing data downloads?

Yes, the skill provides guidance on using ENA's FTP and Aspera services for high-speed bulk data transfer of large files like FASTQ and CRAM.

ENA Bioinformatics & Genomics Data

Name: ENA Bioinformatics & Genomics Data
Author: ricable

byricable

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Ciencia de Datos y ML

Accesses and retrieves nucleotide sequences, raw reads, and genome assemblies from the European Nucleotide Archive (ENA) via REST APIs and FTP.

Acerca de

This skill empowers Claude to interact directly with the European Nucleotide Archive (ENA), a leading global repository for genomics data. It provides the capabilities to query complex metadata, retrieve raw sequencing reads (FASTQ), access genome assemblies, and fetch taxonomic information. Designed for bioinformatics workflows, it helps researchers and developers automate data retrieval, integrate ENA datasets into analysis pipelines, and navigate the ENA's hierarchical data structure including Studies, Samples, Experiments, and Runs, while adhering to best practices for rate limiting and data citation.

Características Principales

Programmatic access to DNA/RNA sequences and raw sequencing reads
Advanced metadata searching via ENA Portal and Browser APIs
1 GitHub stars
Support for multiple data formats including FASTQ, FASTA, and XML
Automated taxonomic information and lineage lookup
Retrieval of genome assemblies and functional annotations

Casos de Uso

Searching for and filtering sequencing samples based on metadata or taxonomy
Automating the download of specific datasets for bioinformatics pipelines
Retrieving reference sequences and annotations for comparative genomic analysis

Acerca de

Características Principales

Programmatic access to DNA/RNA sequences and raw sequencing reads
Advanced metadata searching via ENA Portal and Browser APIs
1 GitHub stars
Support for multiple data formats including FASTQ, FASTA, and XML
Automated taxonomic information and lineage lookup
Retrieval of genome assemblies and functional annotations

Casos de Uso

Searching for and filtering sequencing samples based on metadata or taxonomy
Automating the download of specific datasets for bioinformatics pipelines
Retrieving reference sequences and annotations for comparative genomic analysis