ena-database

# 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 ```bash 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` - B...