ena-database

# ENA Database ## Overview The European Nucleotide Archive (ENA) is a comprehensive public repository for nucleotide sequence data and associated metadata. Access and query DNA/RNA sequences, raw reads, genome assemblies, and functional annotations through REST APIs and FTP for genomics and bioinformatics pipelines. ## When to Use This Skill This skill should be used when: - Retrieving nucleotide sequences or raw sequencing reads by accession - Searching for samples, studies, or assemblies by metadata criteria - Downloading FASTQ files or genome assemblies for analysis - Querying taxonomic information for organisms - Accessing sequence annotations and functional data - Integrating ENA data into bioinformatics pipelines - Performing cross-reference searches to related databases - Bulk downloading datasets via FTP or Aspera ## Core Capabilities ### 1. Data Types and Structure ENA organizes data into hierarchical object types: **Studies/Projects** - Group related data and control release dates. Studies are the primary unit for citing archived data. **Samples** - Represent units of biomaterial from which sequencing libraries were produced. Samples must be registered before submitting most data types. **Raw Reads** - Consist of: - **Experiments**: Metadata about sequencing methods, library preparation, and instrument details - **Runs**: References to data files containing raw sequencing reads from a single sequencing run **Assemblies** - Genome, transcriptome, metageno...