| name | sra-ena |
| description | Fetch and cite public shotgun metagenomic reads from NCBI SRA and EBI ENA. Use this skill when: (1) Downloading public metagenomes by SRR/ERR/DRR, (2) Resolving BioProject/Study accessions, (3) Choosing fasterq-dump vs ena-ftp / Aspera, (4) Building manifests for reanalysis. Upstream: https://github.com/ncbi/sra-tools and https://www.ebi.ac.uk/ena. For analysed microbiome studies and MAG catalogues, use mgnify. For database routing, use public-databases.
|
| license | MIT |
| category | utilities |
| tags | ["database","SRA","ENA","download","reanalysis"] |
| upstream | https://github.com/ncbi/sra-tools |
NCBI SRA / EBI ENA
Upstream: ncbi/sra-tools ·
ENA: https://www.ebi.ac.uk/ena ·
NCBI SRA: https://www.ncbi.nlm.nih.gov/sra
Analytical thinking
SRA/ENA hold raw (or submitted) sequencing data, not polished community
tables. Reanalysis still requires your own QC (fastp, kneaddata) — public
“clean” claims are not transferable without provenance.
Prefer ENA FTP/Aspera for large European-hosted studies when NCBI is slow;
prefer fasterq-dump when you already live in the SRA Toolkit ecosystem.
Always map Study / BioProject → Sample → Run before bulk download so PE
pairs and metadata stay aligned.
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| Accession | SRR/ERR/DRR or BioProject | Manifest TSV with sample IDs |
| Tooling | prefetch + fasterq-dump or wget/curl ENA FTP | ascp for large cohorts |
| Disk | ~2–3× compressed run size | Separate seq/public/ tree |
How to run (SRA Toolkit)
conda install -c bioconda sra-tools
prefetch SRR000001
fasterq-dump --split-files --threads 8 -O seq/public SRR000001
gzip seq/public/SRR000001_*.fastq
How to run (ENA FTP pattern)
wget -c -P seq/public \
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/.../ERR000001_1.fastq.gz \
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/.../ERR000001_2.fastq.gz
Use the ENA browser or API to resolve the exact FTP path; do not invent paths.
Key metadata to archive
| Field | Why |
|---|
| Run accession | Primary download key |
| BioSample / Sample | Biological unit |
| BioProject / Study | Cohort identity |
| Instrument / layout | PE vs SE; chemistry |
| Spot/bases | Depth sanity check |
| Download date + MD5 | Provenance |
Decision tree
Public data needed?
├─ Raw reads for reanalysis → sra-ena
├─ Pre-analysed MGnify study / biome MAG catalogue → mgnify
└─ Reference taxonomy genomes → gtdb
Verify
seqkit stats seq/public/*_{1,2}.fastq.gz
Related skills
public-databases · mgnify · study-design · fastp · kneaddata · setup
