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, metagenome, or metatranscriptome assemblies at various completion levels.

Sequences - Assembled and annotated sequences stored in the EMBL Nucleotide Sequence Database, including coding/non-coding regions and functional annotations.

Analyses - Results from computational analyses of sequence data.

Taxonomy Records - Taxonomic information including lineage and rank.

2. Programmatic Access

ENA provides multiple REST APIs for data access. Consult references/api_reference.md for detailed endpoint documentation.