ENA Sequence Read Archive Metadata Scraper

Scrape sequencing runs, studies and samples from the European Nucleotide Archive (ENA) — including direct FASTQ download links — straight into a clean, structured dataset.

Powered by the free, public ENA Portal API (https://www.ebi.ac.uk/ena/portal/api). No API key, no login, no token. Filter by organism (NCBI taxon), library strategy, or any raw ENA query expression.

The FASTQ links returned are ENA's own public download URLs — they point straight at the raw sequence files on the EBI FTP servers.

What you get

Three modes, selected with the mode input:

• runs — sequencing runs (read_run). Rich metadata plus the actual FASTQ file URLs, sizes and MD5 checksums (split out of ENA's semicolon lists, paired-end aware).
• studies — studies / projects (study).
• samples — biological samples (sample).

Example output (runs)

{
  "type": "read_run",
  "run_accession": "DRR000539",
  "experiment_accession": "DRX000200",
  "sample_accession": "SAMD00011100",
  "study_accession": "PRJDA36577",
  "scientific_name": "Homo sapiens",
  "tax_id": "9606",
  "instrument_platform": "ILLUMINA",
  "instrument_model": "Illumina Genome Analyzer II",
  "library_strategy": "WGS",
  "library_source": "GENOMIC",
  "library_layout": "PAIRED",
  "read_count": 12345678,
  "base_count": 987654321,
  "fastq_urls": [
    "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000539/DRR000539_1.fastq.gz",
    "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000539/DRR000539_2.fastq.gz"
  ],
  "fastq_file_count": 2,
  "fastq_bytes": [51328587, 102162121],
  "total_fastq_bytes": 153490708,
  "fastq_md5": ["dcf9a4f09a386d5e661c53611bb64610", "56002911767c227267ff15a7c3abe84d"],
  "first_public": "2011-02-01",
  "center_name": "RIKEN",
  "study_title": "Human whole genome sequencing",
  "url": "https://www.ebi.ac.uk/ena/browser/view/DRR000539",
  "source": "ena",
  "scraped_at": "2026-08-11T00:00:00+00:00"
}

Input

Field	Type	Description
mode	select	runs, studies or samples. Default runs.
taxonId	string	NCBI taxon ID, e.g. 9606 (human). Builds tax_eq().
freeQuery	string	Raw ENA query expression. Overrides taxonId. e.g. tax_tree(2) AND instrument_platform="OXFORD_NANOPORE".
libraryStrategy	string	e.g. WGS, WXS, RNA-Seq, ChIP-Seq. AND-ed onto the query.
maxItems	integer	Cap on records returned. Default 200, max 10000.

Use cases

• Genomics data discovery — find all public runs for an organism, platform or assay.
• Pipeline input staging — grab FASTQ URLs + sizes + MD5s to seed a bioinformatics pipeline.
• Metadata harvesting — build a catalogue of studies, samples and runs for a taxon.
• Reproducibility — snapshot the exact accessions, checksums and provenance behind an analysis.

Pricing

Roughly ~$0.50 per 1,000 records on Apify's pay-per-result model. The ENA Portal API itself is free; you only pay for Apify platform usage.

Related actors

• NCBI Genomes Scraper
• NCBI E-utilities Scraper
• Ensembl Scraper
• UniProt Scraper

Notes

• Data comes from the ENA Portal API; ENA is maintained by EMBL-EBI.
• FASTQ URLs are public EBI FTP download links.
• This actor reads only public metadata and adds no authentication.