ena-database

To retrieve raw sequencing reads and FASTQ files from ENA, use the REST API to query the European Nucleotide Archive by specific accession numbers. This programmatic access fetches raw reads and genome assemblies directly for downstream bioinformatics pipelines.

Yes, you can query ENA metadata for studies, samples, and experiments using the Taxonomy API and Portal API. It supports searching nucleotide data with various metadata criteria and taxonomic information to filter genomics results.

The best way to integrate ENA nucleotide sequence retrieval into a genomics pipeline is via the REST APIs and FTP. This enables programmatic access to fetch sequences and genome assemblies directly within automated bioinformatics workflows.

No external dependencies are required to access the European Nucleotide Archive API. The Skill integrates directly with ENA's Portal API, Browser API, and Taxonomy API via standard REST calls for nucleotide data retrieval.

Use the ENA FTP endpoint instead of the REST API for bulk downloading large nucleotide datasets like raw reads and genome assemblies. FTP is suited for comprehensive data transfers, while REST APIs handle targeted sequence retrieval by accession.