Agent skill · DevOps & Cloud

bio-sra-data

Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror. Use when pulling FASTQ for SRR/ERR/DRR accessions, deciding between SRA-direct, ENA mirror, or AWS/GCP cloud mirror (STRIDES), handling --include-technical for 10x and other single-cell records, validating with MD5/vdb-validate, navigating SRR/SRX/SRS/SRP/PRJNA hierarchy, or finding accessions via pysradb. Encodes SRA cloud-egress economics, the fasterq-dump uncompressed-scratch trap, and the --max-size default that silently truncates large prefetches.

BioTender-maxgithub.com/BioTender-maxGitHub ↗
claude-codeships scriptsNOASSERTION
Install
npx skills add BioTender-max/awesome-bio-agent-skills --skill sra-data --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 6
SKILL.md size: 16 KB
Bundled scripts: yes
Path: skills/bioskills/sra-data/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 135
Language: Python

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

From the SKILL.md

## Version Compatibility Reference examples tested with: sra-tools 3.0+ (fasterq-dump, prefetch, vdb-validate, vdb-config), pysradb 2.2+, ENA portal API 2.0+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `fasterq-dump --version`, `prefetch --version` - Python: `pip show pysradb` If a flag is unrecognized or behavior changes, run `<tool> --help` and adapt. # SRA Data **"Download FASTQ from this SRA accession"** -> Two paths exist in 2026: the **SRA toolkit** (NCBI's official, with prefetch + fasterq-dump) and the **ENA mirror** (EMBL-EBI's mirror with direct FASTQ download, often faster). For >1 TB workflows, a third path: **AWS Open Data** (STRIDES program) where same-region EC2 pulls SRA data with zero egress cost. The single most impactful decision is **where to pull from**. SRA-direct is the default but ENA is faster more often than not, and AWS Open Data is the right answer for cloud-native analysis pipelines. - CLI: `prefetch SRR...`, `fasterq-dump SRR...`, `vdb-validate SRR...` (sra-tools) - CLI: `curl https://ftp.sra.ebi.ac.uk/...` (ENA mirror; direct FASTQ) - CLI: `aws s3 cp s3://sra-pub-run-odp/sra/SRR.../SRR... ./SRR....sra ...` (

What's inside
Steps it walks through
  1. Version Compatibility
  2. Required Setup
  3. Decision matrix: where to pull from
  4. SRA accession hierarchy
  5. fasterq-dump vs fastq-dump
  6. prefetch and the --max-size trap
  7. ENA mirror: direct FASTQ URLs
  8. Single-cell / 10x quirks
  9. MD5 / vdb-validate
  10. Cloud (STRIDES) access
  11. Code patterns
  12. Single SRR via ENA mirror (preferred default)
  13. prefetch + fasterq-dump (SRA toolkit, classic)
  14. Batch via pysradb metadata
Ships with 5 files
  • examples/download_batch.sh
  • examples/download_single.sh
  • examples/find_sra_runs.py
  • examples/prefetch_large.sh
  • usage-guide.md
Commands it runs
sra-tools (toolkit)
conda install -c bioconda sra-tools           # 3.0+
fasterq-dump --version                        # confirm
Configure cache location (default ~/ncbi/ -- often too small)
vdb-config --cfg                              # show current config
vdb-config --set /repository/user/main/public/root=/data/sra_cache
pip install pysradb
AWS CLI (no NCBI auth needed for public buckets)
aws s3 ls s3://sra-pub-run-odp/sra/SRR12345678/ --no-sign-request
prefetch SRR12345678
More from awesome-bio-agent-skills
All skills →
bio-toolsBiology research tools reference. Always available inside agent containers.AI & Agentssec-reportSEC (size-exclusion chromatography) analysis with peak detection, oligomer classification, and…Code Review & Qualitybio-methylation-callingExtract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates…Data & Analyticsbio-small-rna-seq-mirdeep2-analysisDiscover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small…Data & Analyticsreport-templatePublication-quality PDF report generation using Typst templates. Produces professional scientific…Code Review & Qualitybio-variant-callingCall SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting…Other
About this skill
What does the bio-sra-data skill do?

Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror. Use when pulling FASTQ for SRR/ERR/DRR accessions, deciding between SRA-direct, ENA mirror, or AWS/GCP cloud mirror (STRIDES), handling --include-technical for 10x and other single-cell records, validating with MD5/vdb-validate, navigating SRR/SRX/SRS/SRP/PRJNA hierarchy, or finding accessions via pysradb. Encodes SRA cloud-egress economics, the fasterq-dump uncompressed-scratch trap, and the --max-size default that silently truncates large prefetches.

How do I install it?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill sra-data --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.

Where does this skill come from?

From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.

Is a popular skill a good skill?

Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.

Keep going
All skills →
The full catalog, by category and by tool.
Open Source Radar →
The repositories these skills come from, watched daily.
The people behind them →
Makers and builders across the ecosystem.