bio-sra-data

75 / 100 · Review before installing

Check before installing. Some of what it can do is expected: a data skill usually connects to databases or online services with your credentials.

By lilinji/GeneTind-Life-Skills (GitHub) · data · 17 stars · scanned at commit 908229c

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…

Works with any agent that supports SKILL.md skills.

What this skill can do

Sends data to these websites: ftp.sra.ebi.ac.uk, www.ebi.ac.uk, ${url}

The author does not mention this. Expected for a data skill.

Found in 7 places.

skills/bio-sra-data/SKILL.md, line 25- CLI: `curl https://ftp.sra.ebi.ac.uk/...` (ENA mirror; direct FASTQ)
skills/bio-sra-data/SKILL.md, line 111curl 'https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRR12345678&result=read_run&fields=fastq_ftp,fastq_md5,read_count&format=tsv'
skills/bio-sra-data/SKILL.md, line 118curl -O 'https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR123/078/SRR12345678/SRR12345678_1.fastq.gz'

Show 4 more

skills/bio-sra-data/SKILL.md, line 185META=$(curl -s "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=${SRR}&result=read_run&fields=fastq_ftp,fastq_md5&format=tsv" | tail -1)
skills/bio-sra-data/SKILL.md, line 194curl -sL -o "${fname}" "https://${url}"
skills/bio-sra-data/examples/download_batch.sh, line 31META=$(curl -fsS "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=${ACC}&result=read_run&fields=fastq_ftp,fastq_md5,read_count&format=tsv" | tail -1)
skills/bio-sra-data/examples/download_batch.sh, line 52if ! curl -fsSL -o "${fname}" "https://${url}"; then

Runs commands on your computer

The author does not mention this.

Found in 12 places.

skills/bio-sra-data/SKILL.md, line 33conda install -c bioconda sra-tools # 3.0+
skills/bio-sra-data/SKILL.md, line 47aws s3 ls s3://sra-pub-run-odp/sra/SRR12345678/ --no-sign-request
skills/bio-sra-data/SKILL.md, line 98prefetch SRR12345678

Show 9 more

skills/bio-sra-data/SKILL.md, line 111curl 'https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRR12345678&result=read_run&fields=fastq_ftp,fastq_md5,read_count&format=tsv'
skills/bio-sra-data/SKILL.md, line 118curl -O 'https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR123/078/SRR12345678/SRR12345678_1.fastq.gz'
skills/bio-sra-data/SKILL.md, line 129fasterq-dump SRR12345678 --include-technical --split-files -p -O ./fastq/
skills/bio-sra-data/SKILL.md, line 143vdb-validate SRR12345678
skills/bio-sra-data/SKILL.md, line 157aws s3 ls s3://sra-pub-run-odp/sra/SRR12345678/ --no-sign-request
skills/bio-sra-data/SKILL.md, line 180SRR="${1:-SRR12345678}"
skills/bio-sra-data/SKILL.md, line 209SRR="${1:-SRR12345678}"
skills/bio-sra-data/SKILL.md, line 279SRR="${1:-SRR12345678}"
skills/bio-sra-data/SKILL.md, line 295SRR="${1:-SRR_10x_run}"

Downloads and installs other software

The author does not mention this.

Found in 3 places.

skills/bio-sra-data/SKILL.md, line 41pip install pysradb
skills/bio-sra-data/examples/find_sra_runs.py, line 36print('pysradb not installed; pip install pysradb')
skills/bio-sra-data/usage-guide.md, line 11pip install pysradb # optional, for metadata

Safer alternatives

Low-risk skills in the same category (data) that look related. Check that one does what you need.

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-sra-data' ] || [ -L ~/.agents/skills/'bio-sra-data' ]; then echo 'A skill folder named bio-sra-data already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-sra-data' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-sra-data' ~/.agents/skills/'bio-sra-data' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-sra-data' ~/.claude/skills/'bio-sra-data' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-11	`908229c`	75

Also found in

Identical copies of this skill exist at:

BioTender-max/awesome-bio-agent-skills/skills/bioskills/sra-data