alterlab-ena

To retrieve nucleotide sequence data from ENA, you can use the Portal API or Browser API to search for studies, samples, runs, and assemblies, retrieving results in formats like JSON, TSV, or XML.

When downloading raw reads and genome assemblies from ENA, available sequence data formats include FASTA, FASTQ, and EMBL. Metadata can be retrieved in JSON, TSV, or XML formats via FTP or Aspera.

Yes, you can cross-reference taxonomy records and samples using the ENA Taxonomy REST API and the Cross-Reference Service to link studies, samples, and runs across different database records.

For bulk genomics data access from ENA, use FTP or Aspera for large file transfers. The enaBrowserTools provides command-line utilities to automate and structure bulk downloads reliably.

Yes, programmatic ENA API access includes rate-limiting guidance to ensure reliable integration. Structured querying patterns are provided to maintain consistent API access without exceeding request thresholds.

You can search for sequencing runs by study accession using the ENA Portal API by applying a structured query with the study_accession parameter, returning matching run metadata in your specified format.