European Nucleotide Archive (ENA) API

Overview

The European Nucleotide Archive (ENA) at EMBL-EBI is one of the three global nucleotide sequence databases (with NCBI GenBank and DDBJ). It provides access to raw sequencing reads, assembled sequences, and functional annotations from all organisms. The API supports accession lookup, text search, and bulk data retrieval. Free, no authentication required.

API Endpoints

Portal API (Search)

# Search for studies
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=CRISPR+cas9&result=study&limit=20&format=json"

# Search for samples
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=human+gut+microbiome&result=sample&limit=20&format=json"

# Search for runs (sequencing data)
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=RNA-seq+cancer&result=read_run&limit=20&format=json"

Browser API (Accession Lookup)

# Get record by accession
curl "https://www.ebi.ac.uk/ena/browser/api/xml/PRJEB12345"

# Get in JSON format
curl "https://www.ebi.ac.uk/ena/browser/api/summary/PRJEB12345"

# Get sequence in FASTA
curl "https://www.ebi.ac.uk/ena/browser/api/fasta/AF123456"

# Get in EMBL flat file format
curl "https://www.ebi.ac.uk/ena/browser/api/embl/AF123456"

Taxonomy Search

# Search by organism
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=tax_tree(9606)&result=study&limit=20&format=json"

# Get taxonomy details
curl "https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/9606"

Result Types

Type	Description	Example accession
study	Research project	PRJEB12345
sample	Biological sample	SAMEA12345
experiment	Library/protocol	ERX12345
read_run	Sequencing run	ERR12345
analysis	Computed analysis	ERZ12345
sequence	Assembled sequence	AF123456
wgs_set	Whole genome shotgun	AABR00000000

Query Parameters

Parameter	Description	Example
query	Search text or taxonomy	query=SARS-CoV-2
result	Result type	result=study
limit	Max results (default 100K)	limit=50
offset	Pagination offset	offset=100
format	Response format	json, tsv, xml
fields	Specific fields	fields=accession,description

Python Usage

import requests

PORTAL_URL = "https://www.ebi.ac.uk/ena/portal/api"
BROWSER_URL = "https://www.ebi.ac.uk/ena/browser/api"


def search_studies(query: str, limit: int = 20) -> list:
    """Search ENA for research studies."""
    params = {
        "query": query,
        "result": "study",
        "limit": limit,
        "format": "json",
        "fields": "study_accession,study_title,study_description,"
                  "tax_id,scientific_name,center_name",
    }
    resp = requests.get(f"{PORTAL_URL}/search", params=params)
    resp.raise_for_status()
    return resp.json()


def search_runs(query: str, limit: int = 20) -> list:
    """Search for sequencing runs."""
    params = {
        "query": query,
        "result": "read_run",
        "limit": limit,
        "format": "json",
        "fields": "run_accession,experiment_title,instrument_platform,"
                  "library_strategy,read_count,base_count",
    }
    resp = requests.get(f"{PORTAL_URL}/search", params=params)
    resp.raise_for_status()
    return resp.json()


def get_fasta(accession: str) -> str:
    """Retrieve sequence in FASTA format."""
    resp = requests.get(f"{BROWSER_URL}/fasta/{accession}")
    resp.raise_for_status()
    return resp.text


def get_study_runs(study_accession: str) -> list:
    """Get all sequencing runs for a study."""
    params = {
        "query": f'study_accession="{study_accession}"',
        "result": "read_run",
        "format": "json",
        "fields": "run_accession,fastq_ftp,read_count,base_count",
        "limit": 1000,
    }
    resp = requests.get(f"{PORTAL_URL}/search", params=params)
    resp.raise_for_status()
    return resp.json()


# Example: find COVID-19 sequencing studies
studies = search_studies("SARS-CoV-2 whole genome", limit=5)
for s in studies:
    print(f"{s['study_accession']}: {s['study_title']}")
    print(f"  Organism: {s.get('scientific_name')}")

# Example: find RNA-seq runs
runs = search_runs("RNA-seq breast cancer", limit=5)
for r in runs:
    reads = int(r.get("read_count", 0))
    print(f"{r['run_accession']}: {r.get('experiment_title', '')}")
    print(f"  Platform: {r.get('instrument_platform')} | "
          f"Reads: {reads:,}")

Data Access

# Download FASTQ files (from run metadata)
# The fastq_ftp field provides FTP paths:
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR123/ERR123456/ERR123456_1.fastq.gz

# Bulk download via Aspera (faster)
ascp -QT -l 300m -P33001 \
  era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/ERR123/ERR123456/ ./

References

• ENA
• ENA Portal API
• ENA Browser API
• Harrison, P.W. et al. (2021). "The European Nucleotide Archive in 2020." NAR 49(D1).