Skill: Search ENA

Use When

A user wants to find sequencing data in the European Nucleotide Archive (ENA) hosted at ebi.ac.uk.
A user needs to look up ENA/SRA accessions: PRJEB/PRJNA (study), ERS/SRS (sample), ERX/SRX (experiment), ERR/SRR (run).
A user wants to query ENA by organism, tissue, assay type, instrument, library strategy, or free-text keyword.
A user wants structured metadata (TSV/JSON) for runs or samples in a study without installing any software.
A user needs FASTQ or BAM download URLs (FTP or HTTPS) for ENA runs.
A user wants to find public datasets equivalent to those in NCBI SRA (ENA mirrors most SRA submissions).

Required:
- one of: ENA/SRA accession (PRJEB/PRJNA/ERR/SRR/ERS/SRS/ERX/SRX), free-text search query, or taxonomy ID
Optional:
- result type (ENA entity): study, sample, experiment, run, analysis (default: run)
- organism filter (scientific name or NCBI taxonomy ID)
- library strategy filter (e.g., RNA-Seq, WGS, AMPLICON, ChIP-Seq)
- instrument platform filter (e.g., ILLUMINA, OXFORD_NANOPORE, PACBIO_SMRT)
- library layout: PAIRED or SINGLE
- fields to return (comma-separated ENA field names, or all for full metadata)
- date range: first_public range in YYYY-MM-DD
- maximum results (limit, default 100)
- output format: tsv or json
- output file path

Construct an ENA Portal API search request:
```
GET https://www.ebi.ac.uk/ena/portal/api/search
  ?result=<result-type>
  &query=<lucene-query>
  &fields=<field-list>
  &format=<tsv|json>
  &limit=<n>
```
- For accession-based lookup: query=study_accession="<PRJEB>" or query=run_accession="<ERR>"
- For text search: query=<term> with optional field qualifiers such as scientific_name="Homo sapiens"
- For taxonomy: query=tax_eq(<taxon_id>) or query=tax_tree(<taxon_id>) (includes descendants)
Recommended field sets by result type:
- run: run_accession,experiment_accession,sample_accession,study_accession,scientific_name,instrument_platform,library_strategy,library_layout,read_count,base_count,fastq_ftp,fastq_bytes,first_public
- study: study_accession,secondary_study_accession,study_title,tax_id,scientific_name,study_description,first_public
- sample: sample_accession,secondary_sample_accession,scientific_name,tax_id,sample_title,collection_date,country,tissue_type
Parse the response to build a summary table.
Extract fastq_ftp or fastq_aspera columns for direct download links.
For large queries (>1000 runs), use limit and offset for paging, or stream with format=tsv.
Report download commands using wget or curl for the FTP URLs.

API request URL used
Number of matching records
Summary table with key fields per result type (accession, organism, strategy, platform, read count, size, date)
FASTQ download URLs (FTP and HTTPS) for run-level queries
Saved output files when a path is provided:
- results.tsv or results.json
- fastq_urls.txt (one URL per line, ready for wget -i or aria2c -i)

This skill depends on live access to https://www.ebi.ac.uk/ena/portal/api/.
ENA Portal API returns at most 100 000 rows per request; use paging for larger result sets.
Not all SRA submissions are mirrored in ENA immediately; newly submitted data may not be available yet.
Controlled-access datasets (e.g., from EGA) are not accessible through the ENA Portal API.
The fastq_ftp field may be empty for runs that are only available as SRA format; in that case fall back to sra_ftp or use fasterq-dump.
ENA Lucene query syntax differs from NCBI E-utilities query syntax; do not mix them.
Common failure cases:
- using NCBI-style [field] tag syntax instead of ENA field="value" syntax
- requesting result=run but filtering by study-level fields not propagated to run records
- fastq_ftp returning multiple semicolon-separated URLs (for paired-end runs); must split on ;
- omitting tax_tree() and only getting exact taxon matches, missing subspecies/strains