ena-database

You can retrieve raw FASTQ reads from ENA by querying the Portal and Browser APIs with a specific run accession to fetch file download URLs and metadata. The Skill recommends FTP or Aspera patterns for efficiently downloading large sequencing datasets.

Yes, you can use the ENA Portal API for targeted discovery of studies, samples, and analyses based on metadata criteria. This allows you to filter and retrieve specific nucleotide records before downloading the associated sequence or assembly files.

ENA API sequence retrieval requires handling HTTP 429 rate limits by implementing batching and retry with exponential backoff. This ensures programmatic queries against Portal, Browser, and Taxonomy endpoints return correct accession-scoped results without interruption.

The best way to get taxonomy lineage details is to query the dedicated ENA Taxonomy endpoint using the associated accession or taxon identifier. This navigates cross-references and returns lineage records for use in genomics and bioinformatics pipelines.

To download large assembled genomes and raw sequencing datasets from ENA, the Skill retrieves file download URLs via the API and recommends FTP/Aspera transfer workflows. This bulk retrieval approach is necessary for handling large-scale bioinformatics pipelines efficiently.