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ena-database

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Access the European Nucleotide Archive (ENA) via REST APIs and FTP/Aspera to search and retrieve sequences, raw reads (FASTQ), assemblies, and metadata when you have accession IDs or need metadata-driven discovery for genomics pipelines.

scientific-skills/Evidence Insight/ena-database/SKILL.md

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

Use this skill when you need to:

1. Download raw sequencing reads (FASTQ) for a run/experiment/study using ENA accessions (e.g., `ERR...`, `SRR...`, `PRJ...`).
2. Find samples, runs, experiments, or assemblies by metadata filters (organism, platform, collection date, geography, etc.).
3. Retrieve record metadata (XML/JSON/TSV) for reproducible reporting and pipeline inputs.
4. Query taxonomic lineage/rank for organisms to drive filtering or grouping in analyses.
5. Perform bulk discovery + bulk download workflows (search first, then fetch many files via FTP/Aspera/tools).

## Key Features

- **Multi-object ENA coverage**: studies/projects, samples, experiments, runs, assemblies, sequences, analyses, taxonomy records.
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