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.
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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.
This skill should be used when:
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:
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.
ENA provides multiple REST APIs for data access. Consult references/api_reference.md for detailed endpoint documentation.
Key APIs:
ENA Portal API - Advanced search functionality across all ENA data types
ENA Browser API - Direct retrieval of records and metadata
ENA Taxonomy REST API - Query taxonomic information
ENA Cross Reference Service - Access related records from external databases
CRAM Reference Registry - Retrieve reference sequences
Rate Limiting: All APIs have a rate limit of 50 requests per second. Exceeding this returns HTTP 429 (Too Many Requests).
Browser-Based Search:
Programmatic Queries:
Example API Query Pattern:
import requests
# Search for samples from a specific study
base_url = "https://www.ebi.ac.uk/ena/portal/api/search"
params = {
"result": "sample",
"query": "study_accession=PRJEB1234",
"format": "json",
"limit": 100
}
response = requests.get(base_url, params=params)
samples = response.json()
Metadata Formats:
Sequence Data:
Download Methods:
Retrieve raw sequencing reads by accession:
# Download run files using Browser API
accession = "ERR123456"
url = f"https://www.ebi.ac.uk/ena/browser/api/xml/{accession}"
Search for all samples in a study:
# Use Portal API to list samples
study_id = "PRJNA123456"
url = f"https://www.ebi.ac.uk/ena/portal/api/search?result=sample&query=study_accession={study_id}&format=tsv"
Find assemblies for a specific organism:
# Search assemblies by taxonomy
organism = "Escherichia coli"
url = f"https://www.ebi.ac.uk/ena/portal/api/search?result=assembly&query=tax_tree({organism})&format=json"
Get taxonomic lineage:
# Query taxonomy API
taxon_id = "562" # E. coli
url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/{taxon_id}"
Bulk Download Pattern:
BLAST Integration: Integrate with EBI's NCBI BLAST service (REST/SOAP API) for sequence similarity searches against ENA sequences.
Rate Limiting:
Data Citation:
API Response Handling:
Performance:
This skill includes detailed reference documentation for working with ENA:
api_reference.md - Comprehensive API endpoint documentation including:
Load this reference when constructing complex API queries, debugging API responses, or needing specific parameter details.
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