What is bio-sra-data?

A guide to downloading raw sequencing reads from the NCBI Sequence Read Archive, a public database of sequencing experiments. It covers the SRA Toolkit, the ENA mirror, and cloud copies of the same data.

Use it to turn SRA accessions into FASTQ files, check downloads, and retrieve sequencing data from NCBI, ENA, or cloud storage.

It helps choose a practical download route, validate files, and handle large datasets or technical reads from single-cell experiments.

bio-sra-data — Skill for Claude Code and Codex by GPTomics

Install

Getting it into your agent

It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.

Clone the repo

git clone --depth 1 https://github.com/GPTomics/bioSkills

agentmods

npx agentmods add skills/gptomics/bioskills/sra-data

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gptomics/bioskills/sra-data/github.svg)](https://agentmods.dev/skills/gptomics/bioskills/sra-data)

Your own site

<a href="https://agentmods.dev/skills/gptomics/bioskills/sra-data"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/sra-data/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/gptomics/bioskills/sra-data"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/sra-data.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 158 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 4,658 The whole file, excluding the scripts and references it only reads on demand.

Security scan C 2 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00158	$0.04658
Opus 5	$0.00079	$0.02329
Sonnet 5	$0.00032	$0.00932
Haiku 4.5	$0.00016	$0.00466

Measured 9d ago against content hash 9264904f149b, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade C, and why

bio-sra-data scanned grade C with 2 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.

The scan reads SKILL.md. This mod also ships 4 executable files (examples/download_batch.sh, examples/download_single.sh, examples/find_sra_runs.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Recursive force deletehighDestructive command

rm -rf with a variable or a broad path is one typo away from removing the wrong tree.

# rm -rf ~/ncbi/sra/${SRR}.sra

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

- CLI: `curl https://ftp.sra.ebi.ac.uk/...` (ENA mirror; direct FASTQ)

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

bio-sra-data — 94% identical, 16 lines differ

database-access/sra-data/SKILL.md · 378 lines

How it starts

The opening of the file, as written. The whole thing — 378 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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 ... (STRIDES; object is unsuffixed; same-region free)
Python: pysradb for metadata; subprocess for download

Required Setup

# 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

# Optional: pysradb for metadata
pip install pysradb

For STRIDES cloud:

# AWS CLI (no NCBI auth needed for public buckets)
aws s3 ls s3://sra-pub-run-odp/sra/SRR12345678/ --no-sign-request

Decision matrix: where to pull from

Source	When best	Speed	Cost
ENA mirror (FTP/Aspera)	Default for most workflows	Often fastest; direct FASTQ (no SRA->FASTQ conversion needed)	Free; no rate limit observed
SRA toolkit + AWS STRIDES	Same-region EC2/EKS	Fastest within AWS us-east-1	Free egress within region; small storage cost
SRA toolkit + GCP STRIDES	Same-region GCP Compute Engine	Fastest within GCP us-central1	Free egress within region
SRA-direct (prefetch + fasterq-dump)	On-prem; small downloads; need SRA-format access	Variable; can be slow off-peak fails	Free; NCBI throttles by IP
Aspera (`ascp`)	Institutional accounts only	Faster than HTTPS on long links	NCBI public Aspera retired 2019; ENA public Aspera retired ~2023; institutional use still possible

Read the full file on GitHub · 378 lines

Files

What ships with it

5 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

9d ago First seen · 378 lines · 158 tokens per session scan C 9264904f149b

Subscribe to this mod's changes

bio-sra-data is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 28d ago), licensed MIT. It adds 158 tokens to every session and 4,658 once invoked, about $0.0008 per session on Opus 5. A static security scan graded it C with 2 findings (recursive force delete, makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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bio-sra-data