ena-database

Retrieve nucleotide sequences and metadata from ENA programmatically by querying the Portal API and Browser API. This supports automated searches for studies, samples, runs, and taxonomic data with XML, JSON, or TSV outputs.

The best way to download raw reads and genome assemblies in bulk from ENA is via FTP or Aspera. This satisfies bulk transfer requirements for FASTQ files and other large genomic datasets efficiently.

Yes, you can fetch taxonomic data and cross-reference related databases using the ENA Portal API. This enables integration of studies, samples, and runs into bioinformatics pipelines for taxonomic lookups.

ENA API programmatic access supports pagination and rate limiting for large queries. This ensures stable retrieval of sequence data and metadata without exceeding request thresholds during automated workflows.

Get FASTQ files for a specific study accession like PRJEB1234 from ENA by querying its accession ID. The API locates associated raw reads and facilitates their download directly through FTP or Aspera.

Available formats when retrieving ENA sequences and run metadata via API include XML, JSON, and TSV. These output formats allow flexible integration of nucleotide data into various downstream bioinformatics applications.