ENA Database — European Nucleotide Archive Programmatic Access

ENA Database — European Nucleotide Archive Programmatic Access

Overview

The European Nucleotide Archive (ENA) is EMBL-EBI's comprehensive nucleotide sequence database, encompassing raw sequencing reads, genome assemblies, annotated sequences, and associated metadata. It mirrors and extends INSDC data (GenBank, DDBJ). All access is via REST APIs with no authentication required.

When to Use

• Searching for sequencing studies, samples, or experiments by organism, project, or keyword
• Downloading raw FASTQ/BAM files for reanalysis of public sequencing datasets
• Retrieving genome assemblies with quality statistics (N50, contig count, genome size)
• Fetching nucleotide sequences in FASTA or EMBL flat-file format by accession
• Exploring taxonomic lineage and finding organisms by partial name
• Cross-referencing ENA records with external databases (ArrayExpress, UniProt, PDB)
• Building bulk download lists for large-scale sequencing projects
• For multi-database Python queries (ENA + UniProt + KEGG), prefer bioservices instead
• For NCBI-specific queries (PubMed literature, GenBank records), use pubmed-database or Biopython Entrez

Prerequisites

pip install requests

API constraints:

• Rate limit: 50 requests per second across all ENA APIs
• No authentication required
• Large result sets: use pagination (limit + offset) or streaming (limit=0 for TSV download)
• Portal API base: https://www.ebi.ac.uk/ena/portal/api
• Browser API base: https://www.ebi.ac.uk/ena/browser/api
• Taxonomy API base: https://www.ebi.ac.uk/ena/taxonomy/rest
• Cross-ref API base: https://www.ebi.ac.uk/ena/xref/rest

Quick Start

import requests
import time

BASE_PORTAL = "https://www.ebi.ac.uk/ena/portal/api"