ena-database - Query and retrieve data from European Nucleotide Archive
Access the European Nucleotide Archive via REST APIs and FTP or Aspera to search and retrieve sequences, raw reads, assemblies, and metadata.
Tags
Updated: 2026-09-19Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Download raw sequencing reads
- Search records using metadata filters
- Retrieve record metadata
- Query taxonomic lineage and rank
- Fetch reference sequences by checksum
Inputs
- Accession IDs
- Metadata search queries
- Taxonomy IDs
- Reference sequence checksums
Outputs
- FASTQ files
- FASTA files
- BAM or CRAM files
- XML, JSON, or TSV metadata
- EMBL flat files
Requirements
- Python >= 3.9
- requests >= 2.31.0
- lxml >= 4.9.0