ena-database

Source: 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