bio-sra-data SKILL.md skillB
bio-sra-data from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-sra-data@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- B, 16 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-database-access-sra-data/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 16,137 bytes
- Repository stars
- 662
- License
- MIT
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…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## 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) …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-sra-data@sha256:19f2d1afe6ef746bThe line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_faqnxwl562vls7t7)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
- fail: No recursive delete of root, home or parent (matched: rm -rf ~/)
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (16137 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Starting a new one? Use a template for SKILL.md on mdpantry, which passes every one of these checks and says what to change in it.
Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_faqnxwl562vls7t7 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-sra-data GET https://markdownregistry.com/api/v1/blob/19f2d1afe6ef746b6a6410090766eaa5924d0c5f397f8956d3adb8284f63c525
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.