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Agent skill

Sragent

by aiskillstore in aiskillstore/marketplace

Query the Sequence Read Archive (SRA), retrieve scientific publications, and analyze genomics metadata using the SRAgent toolkit.

No licenceAuto-check passedResearch & Science

Install Sragent

skills CLI
$ npx skills add aiskillstore/marketplace --skill sragent -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aiskillstore/marketplace sragent --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/arcinstitute/sragent .claude/skills/sragent && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
sragent
GitHub stars
430
Used in
1 other repo
Token cost
~3.5k tokens
SKILL.md length
884 words
Files
7 (incl. references)
Skills in repo
1,044
Repo updated
First seen
Licence
None found

At a glance

Query the Sequence Read Archive (SRA), retrieve scientific publications, and analyze genomics metadata using the SRAgent toolkit.

  • Works in 8 steps: Install SRAgent → Configure environment variables → Configure Settings → …
  • Working with SRA/GEO datasets
  • SKILL.md covers Overview, Setup Instructions, Core Capabilities and When to Use This Skill, plus 4 more sections
  • Calls uv, python and git; reaches ncbi.nlm.nih.gov and github.com; needs CORE_API_KEY and NCBI_API_KEY

What it does

Sragent is an agent skill from aiskillstore/marketplace. Query the Sequence Read Archive (SRA), retrieve scientific publications, and analyze genomics metadata using the SRAgent toolkit. Supports accession conversion (GSE→SRX→SRR), BigQuery metadata queries, manuscript downloads from multiple sources, and scRNA-seq technology identification. Use when working with SRA/GEO datasets, finding publications, or analyzing single-cell sequencing experiments.

Its SKILL.md is about 3.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files, including reference files (for example `README.md`, `references/example-settings.yml` and `references/metadata-fields.md`).

It sits in Research & Science, covering Bioinformatics and Data warehousing. It works with Google BigQuery, NCBI and OpenAI. The repository describes itself as: Security-audited skills for Claude, Codex & Claude Code. One-click install, quality verified.

When your agent uses it

  • Working with SRA/GEO datasets
  • Finding publications
  • Analyzing single-cell sequencing experiments

Example prompts

  • “/sragent”

Requirements

  • Python 3
  • A credential in OPENAI_API_KEY
  • A credential in ANTHROPIC_API_KEY

Workflow steps

8 steps, taken from the step headings in SKILL.md.

  1. Install SRAgent
  2. Configure environment variables
  3. Configure Settings
  4. Verify Setup
  5. Accession Conversion
  6. Metadata Extraction
  7. BigQuery Analysis
  8. Publication Retrieval

What it can do on your machine

Read from SKILL.md and the folder at commit 755bc35. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • uv
    • python
    • git

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • ncbi.nlm.nih.gov
    • github.com

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names these keys or tokens, usually read from environment variables:

    • CORE_API_KEY
    • NCBI_API_KEY
    • OPENAI_API_KEY
    • ANTHROPIC_API_KEY
    • GOOGLE_APPLICATION_CREDENTIALS

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Sragent loads about 3.5k tokens when it runs, and up to ~12k if it reads all its reference files. Until then it costs about 102 tokens; SKILL.md has 884 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~102
When it runs · the whole SKILL.md, loaded when a task matches
~3.5k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~12k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

Without a licence we can't republish the file, so here is its outline and opening line. It has 884 words (~3,509 tokens).

“SRAgent is an agentic workflow system for working with the NCBI Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. It automates literature discovery, metadata extraction, and manuscript retrieval for genomics datasets.”

— opening of SKILL.md by aiskillstore
name
sragent

Read the full SKILL.md on GitHub

Files

SKILL.md and 6 other files (references) in skills/arcinstitute/sragent of aiskillstore/marketplace.

  • SKILL.md
  • README.md
  • references/example-settings.yml
  • references/metadata-fields.md
  • references/quick-reference.md
  • references/usage-examples.md
  • skill-report.json

Open the folder on GitHubat commit 755bc35

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in aiskillstore/marketplace, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Sragent next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Sragent compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Sragent this skillaiskillstore/marketplace4301 repos~3.5kAutomated safety check: PassNone
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0
Biopython Bioinformaticsaiming-lab/AutoResearchClaw15k—~810Automated safety check: PassMIT
Bio Write SequencesGPTomics/bioSkills1.2k3 repos~2.1kAutomated safety check: PassMIT
ETE Toolkit for Phylogenetic Treesdavila7/claude-code-templates32k11 repos~4.5kAutomated safety check: NotesMIT
Biopythondavila7/claude-code-templates32k12 repos~3.4kAutomated safety check: PassMIT

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    Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis.

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Works with

Categories

Questions about Sragent

What does Sragent do?

Query the Sequence Read Archive (SRA), retrieve scientific publications, and analyze genomics metadata using the SRAgent toolkit. Sragent is an agent skill from aiskillstore/marketplace. Query the Sequence Read Archive (SRA), retrieve scientific publications, and analyze genomics metadata using the SRAgent toolkit.

When should I use Sragent?

Sragent fits situations like: working with SRA/GEO datasets; finding publications; analyzing single-cell sequencing experiments.

How do I install Sragent in Claude Code?

Run `npx skills add aiskillstore/marketplace --skill sragent -a claude-code`. Or copy the skill folder (skills/arcinstitute/sragent in aiskillstore/marketplace) into .claude/skills/sragent in your project. Claude Code loads it when a task matches its description.

How do I install Sragent in Codex?

Run `npx skills add aiskillstore/marketplace --skill sragent -a codex`. Or copy the skill folder (skills/arcinstitute/sragent in aiskillstore/marketplace) into .agents/skills/sragent in your project. Codex loads it when a task matches its description.

Can I use Sragent in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aiskillstore/marketplace --skill sragent -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/sragent, .gemini/skills/sragent, .github/skills/sragent and .opencode/skills/sragent in your project.

What does Sragent need to run?

Going by SKILL.md and its folder, Sragent needs the command-line tools its instructions call (uv, python and git) and credentials named CORE_API_KEY, NCBI_API_KEY, OPENAI_API_KEY and ANTHROPIC_API_KEY. Our summary lists: Python 3; A credential in OPENAI_API_KEY; A credential in ANTHROPIC_API_KEY.

Does Sragent access the network?

SKILL.md names 2 domains. In commands or code: ncbi.nlm.nih.gov and github.com; the agent is likely to contact these when it follows the instructions. This is read from the text; nothing was executed.

Is Sragent safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Sragent use?

No licence was found for Sragent or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Sragent use?

About 3.5k tokens (SKILL.md is roughly 14k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 8k tokens, read only when the agent opens those files.

What are the alternatives to Sragent?

Skills that share tags, products or a category with Sragent: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Biopython Bioinformatics (aiming-lab/AutoResearchClaw, 15k stars), Bio Write Sequences (GPTomics/bioSkills, 1.2k stars) and ETE Toolkit for Phylogenetic Trees (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Sragent?

aiskillstore (a GitHub organization) maintains it in aiskillstore/marketplace, which has 430 GitHub stars. The repository holds 1,044 skills in this directory. The repository was last updated on October 9, 2026.

Source: aiskillstore/marketplace on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.