| name | ena-database |
| description | Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats. |
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.
