Agent skill

Ncbi Datasets

Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

Install Ncbi Datasets

skills CLI

$ npx skills add ClawBio/ClawBio --skill ncbi-datasets -a claude-code

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

GitHub CLI

$ gh skill install ClawBio/ClawBio ncbi-datasets --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/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/ncbi-datasets .claude/skills/ncbi-datasets && 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/

Paste into Claude Code

Install the "ncbi-datasets" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/ncbi-datasets into .claude/skills/ncbi-datasets/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ncbi-datasets", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/ClawBio/ClawBio/tree/main/skills/ncbi-datasets

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add ClawBio/ClawBio --skill ncbi-datasets -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio ncbi-datasets --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/ncbi-datasets .agents/skills/ncbi-datasets && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "ncbi-datasets" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/ncbi-datasets into .agents/skills/ncbi-datasets/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ncbi-datasets", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill ncbi-datasets -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio ncbi-datasets --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/ncbi-datasets .cursor/skills/ncbi-datasets && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "ncbi-datasets" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/ncbi-datasets into .cursor/skills/ncbi-datasets/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ncbi-datasets", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/ClawBio/ClawBio.git --path skills/ncbi-datasets

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add ClawBio/ClawBio --skill ncbi-datasets -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio ncbi-datasets --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/ncbi-datasets .gemini/skills/ncbi-datasets && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "ncbi-datasets" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/ncbi-datasets into .gemini/skills/ncbi-datasets/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ncbi-datasets", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install ClawBio/ClawBio ncbi-datasets

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add ClawBio/ClawBio --skill ncbi-datasets -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/ncbi-datasets .github/skills/ncbi-datasets && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "ncbi-datasets" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/ncbi-datasets into .github/skills/ncbi-datasets/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ncbi-datasets", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill ncbi-datasets -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio ncbi-datasets --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/ncbi-datasets .opencode/skills/ncbi-datasets && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "ncbi-datasets" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/ncbi-datasets into .opencode/skills/ncbi-datasets/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ncbi-datasets", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: ncbi-datasets
GitHub stars: 1.2k
Used in: 1 other repo
Token cost: ~2.8k tokens
SKILL.md length: 882 words
Files: 2 (incl. references)
Skills in repo: 104
Repo updated: Oct 7, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

Works in 8 steps: Genome download by taxon or accession —… → Gene sequence retrieval — download by… → Ortholog packages — download ortholog… → …
Tasks that involve Bioinformatics
SKILL.md covers Trigger, Why This Exists, Core Capabilities and Scope, plus 9 more sections
Calls conda

What it does

Ncbi Datasets is an agent skill from ClawBio/ClawBio. Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

Its SKILL.md is about 2.8k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including reference files (for example `references/ncbi-datasets.md`).

It sits in Research & Science, covering Bioinformatics. It works with NCBI. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

Tasks that involve Bioinformatics

Example prompts

“/ncbi-datasets”

Workflow steps

8 steps, taken from the first numbered list in SKILL.md.

Genome download by taxon or accession — fetch FASTA, GFF3, GTF, protein, RNA, CDS, or GenBank flat files for any assembly; filter by…
Gene sequence retrieval — download by NCBI Gene ID, gene symbol, RefSeq accession, locus tag, or entire species; include rna, protein…
Ortholog packages — download ortholog gene sets across custom taxon groups (--ortholog mammals, --ortholog primates, --ortholog all)
Virus sequences — retrieve SARS-CoV-2 and other viral genomes or proteins, filterable by host, collection date, and geographic region
Taxonomy data — download lineage, parent/child relationships, and name reports for any taxon by ID or name
Metadata-only queries — datasets summary returns structured JSON Lines reports; pipe to dataformat tsv for instant TSV tables with custom…
Large-scale dehydrated downloads — download metadata + file manifest only, then parallel-rehydrate actual data with datasets rehydrate…
Preview before downloading — --preview shows package size and file count without transferring data

What it can do on your machine

Read from SKILL.md and the folder at commit 5e045e3. 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:
- conda
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- ncbi.nlm.nih.gov
- doi.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Ncbi Datasets loads about 2.8k tokens when it runs, and up to ~6.5k if it reads all its reference files. Until then it costs about 32 tokens; SKILL.md has 882 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~32
When it runs · the whole SKILL.md, loaded when a task matches: ~2.8k
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~6.5k

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

The full file from ClawBio/ClawBio at commit 5e045e3, republished under its MIT licence (© ClawBio). 882 words, ~2,815 tokens.

Download SKILL.mdSave it as .claude/skills/ncbi-datasets/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.

name: ncbi-datasets
description: Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.
license: MIT
metadata.author: nullvoid42
metadata.domain: datasets
metadata.tags: ncbi, genomics, bioinformatics, genome-download, gene, virus, taxonomy, datasets, dataformat, refseq, genbank
metadata.version: 0.1.0

🦖 Skill Name

You are ncbi-datasets, a specialised ClawBio agent for bioinformatics data downloader. Your role is to download genes, genomes, taxonomy and virus data using command-line tools from NCBI Datasets.

Trigger

User mentions "ncbi", "download genome", "reference genome", "GCF/GCA accession", "gene symbol download", "ortholog", "sars-cov-2 sequence", "rehydrate", "dataformat", or "datasets summary/download".

Why This Exists

Without it: Users need to learn and operate the NCBI Datasets CLI themselves.

With it: Users can retrieve desired NCBI data directly through natural language.

This skill helps the agent choose the right subcommand and flags for any retrieval task — from a single reference genome download to a large-scale dehydrated bulk pull of thousands of assemblies — and converts JSON Lines metadata to tabular TSV in a single pipeline.

Core Capabilities

Genome download by taxon or accession — fetch FASTA, GFF3, GTF, protein, RNA, CDS, or GenBank flat files for any assembly; filter by RefSeq/GenBank, assembly level, annotation status, and release date
Gene sequence retrieval — download by NCBI Gene ID, gene symbol, RefSeq accession, locus tag, or entire species; include rna, protein, cds, 5'/3'-UTR, or product reports
Ortholog packages — download ortholog gene sets across custom taxon groups (--ortholog mammals, --ortholog primates, --ortholog all)
Virus sequences — retrieve SARS-CoV-2 and other viral genomes or proteins, filterable by host, collection date, and geographic region
Taxonomy data — download lineage, parent/child relationships, and name reports for any taxon by ID or name
Metadata-only queries — datasets summary returns structured JSON Lines reports; pipe to dataformat tsv for instant TSV tables with custom field selection
Large-scale dehydrated downloads — download metadata + file manifest only, then parallel-rehydrate actual data with datasets rehydrate --max-workers
Preview before downloading — --preview shows package size and file count without transferring data

Scope

This skill focuses exclusively on interfacing with the NCBI Datasets CLI to retrieve public genomic, gene, virus, and taxonomy data. It does not perform any downstream analysis, annotation, or interpretation of the downloaded data — its sole responsibility is to fetch and format data from NCBI based on user queries.

Workflow

Identify data type — genome, gene, virus, or taxonomy?
Identify search key — taxon name, NCBI Taxonomy ID, assembly accession (GCF/GCA), gene symbol, Gene ID, or RefSeq accession
Choose operation — summary for metadata/TSV only; download for full data packages
Select data types — use --include to limit to genome, rna, protein, cds, gff3, gtf, gbff, seq-report, or none (metadata only)
Apply filters — --reference, --annotated, --assembly-level, --assembly-source, --released-after
For large downloads (≥ 1,000 genomes or > 15 GB) — use --dehydrated, then unzip, then datasets rehydrate
For tabular output — pipe --as-json-lines output through dataformat tsv <report-type> --fields ...

Input Formats

Format	Extension	Required Fields	Example
Accession list	`.txt`	One accession per line	`GCF_000001405.40`
FASTA (input filter)	`.fa`, `.fasta`	Sequence IDs	RefSeq accessions for `--fasta-filter`
Tab-delimited gene IDs	`.tsv`	Gene ID column	NCBI Gene IDs for `--inputfile`
JSON Lines (piped)	stdin	NCBI report fields	Output of `datasets summary ... --as-json-lines`

CLI Reference

Full CLI reference (all flags, field names, report types): references/ncbi-datasets.md

bash

# ── Genome metadata as TSV ────────────────────────────────────────────────────
datasets summary genome taxon human --assembly-source refseq --as-json-lines \
  | dataformat tsv genome --fields accession,assminfo-name,organism-name,assminfo-level

# ── Download reference genome (FASTA + GFF3) ─────────────────────────────────
datasets download genome taxon human --reference --include genome,gff3 \
  --filename human_ref.zip

# ── Download by accession ─────────────────────────────────────────────────────
datasets download genome accession GCF_000001405.40 --filename human_GRCh38.zip

# ── Gene download by symbol ───────────────────────────────────────────────────
datasets download gene symbol BRCA1 --taxon human \
  --include gene,rna,protein --filename brca1.zip

# ── Ortholog download ─────────────────────────────────────────────────────────
datasets download gene gene-id 59272 --ortholog mammals --filename ace2_mammals.zip

# ── Virus download ────────────────────────────────────────────────────────────
datasets download virus genome taxon sars-cov-2 --host dog \
  --filename sarscov2_dog.zip

# ── Taxonomy download ─────────────────────────────────────────────────────────
datasets download taxonomy taxon 'bos taurus' --include names --parents --children

# ── Large-scale dehydrated workflow ──────────────────────────────────────────
datasets download genome accession --inputfile accessions.txt \
  --dehydrated --filename bacteria.zip
unzip bacteria.zip -d bacteria
datasets rehydrate --directory bacteria/ --max-workers 20

# ── Preview without downloading ───────────────────────────────────────────────
datasets download genome taxon human --reference --preview

# ── See ## Demo section for a runnable, zero-auth example ─────────────────────

Demo

To verify the skill works for retrieving yeast reference genome metadata and outputting a TSV summary:

bash

datasets summary genome taxon 'saccharomyces cerevisiae' \
  --reference --as-json-lines \
  | dataformat tsv genome \
  --fields accession,organism-name,assminfo-level,assminfo-release-date

Expected output: one header row followed by one TSV data row per reference assembly; columns match the --fields values in order. Look like this:

Assembly Accession	Organism Name	Assembly Level	Assembly Release Date
GCF_000146045.2	Saccharomyces cerevisiae S288C	Complete Genome	2014-12-17

Show full SKILL.md (344 more words)Show less

Downloaded ZIP file structure

After unzip ncbi_dataset.zip -d my_dataset/, the extracted archive contains:

my_dataset/
├── ncbi_dataset/
│   └── data/
│       ├── dataset_catalog.json          # Package manifest and file index
│       ├── assembly_data_report.jsonl    # Per-assembly metadata (JSON Lines)
│       ├── GCF_000001405.40/
│       │   ├── GCF_000001405.40_GRCh38.p14_genomic.fna   # Genomic FASTA
│       │   ├── genomic.gff               # GFF3 annotation
│       │   ├── protein.faa               # Protein sequences
│       │   ├── rna.fna                   # Transcript sequences
│       │   └── cds_from_genomic.fna      # CDS sequences
│       └── ...                           # Additional accession dirs
└── README.md                             # NCBI usage notes

For gene packages the layout is analogous, with gene.fna, rna.fna, protein.faa, and gene_result.jsonl under each Gene-ID directory.

Dependencies

Required:

datasets CLI v16+ (NCBI Datasets command-line tool)
dataformat CLI v16+ (NCBI JSON Lines → TSV/Excel converter)

Install via conda (recommended — works on macOS, Linux, Windows):

bash

conda install -c conda-forge ncbi-datasets-cli

Install via direct download (macOS / Linux / Windows):

See references/ncbi-datasets.md § Installation for curl commands, or visit the official NCBI install guide.

Optional:

unzip / 7z — for extracting downloaded zip archives

Error handling

Attempt to use --help to retrieve command usage and parameter descriptions
Refer to the NCBI Datasets documentation for further troubleshooting and guidance

Safety

Local-first: All data is downloaded directly from NCBI public servers to the local filesystem; no third-party intermediary stores your queries or results
Public databases only: This skill makes network calls exclusively to api.ncbi.nlm.nih.gov and ftp.ncbi.nlm.nih.gov — both are unauthenticated public endpoints (API key is optional, not required)
No hardcoded paths: All output paths use user-supplied --filename or relative defaults; no absolute paths are embedded
No hallucination: Accession numbers, gene IDs, organism names, and field values are fetched live from NCBI — this skill never invents identifiers or fabricates metadata
Preview before large transfers: Always use --preview before downloading multi-GB packages to confirm scope
Disclaimer: ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a qualified professional before making any clinical or regulatory decisions based on downloaded data.

Citations

NCBI Datasets CLI — Sayers et al. (2022) "Database resources of the National Center for Biotechnology Information." Nucleic Acids Research, 50(D1): D20–D26. https://doi.org/10.1093/nar/gkab1112
NCBI Genome Database — https://www.ncbi.nlm.nih.gov/genome/
NCBI Datasets Documentation - https://www.ncbi.nlm.nih.gov/datasets/docs/v2/
RefSeq — O'Leary et al. (2016) "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation." Nucleic Acids Research, 44(D1): D733–D745. https://doi.org/10.1093/nar/gkv1189
NCBI Gene — https://www.ncbi.nlm.nih.gov/gene/
NCBI Taxonomy — Schoch et al. (2020) "NCBI Taxonomy: a comprehensive update on curation, resources and tools." Database, 2020: baaa062. https://doi.org/10.1093/database/baaa062
NCBI Virus — Hatcher et al. (2017) "Virus Variation Resource – improved response to emergent viral outbreaks." Nucleic Acids Research, 45(D1): D482–D490. https://doi.org/10.1093/nar/gkw1065

Files

SKILL.md and 1 other file (references) in skills/ncbi-datasets of ClawBio/ClawBio.

SKILL.md
references/ncbi-datasets.md

Open the folder on GitHubat commit 5e045e3

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 ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

BioTender-max/awesome-bio-agent-skillsskills/clawbio/ncbi-datasets

Compare with similar skills

Ncbi Datasets 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.

Ncbi Datasets compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Ncbi Datasets this skillClawBio/ClawBio	1.2k	1 repos	~2.8k	Automated safety check: Pass	MIT	yesterday
Dbsnp Databasegoogle-deepmind/science-skills	3.2k	3 repos	~3.4k	Automated safety check: Notes	Apache-2.0	23 days ago
Biopython Bioinformaticsaiming-lab/AutoResearchClaw	15k	—	~810	Automated safety check: Pass	MIT	1 mo ago
Bio Write SequencesGPTomics/bioSkills	1.2k	3 repos	~2.1k	Automated safety check: Pass	MIT	1 mo ago
ETE Toolkit for Phylogenetic Treesdavila7/claude-code-templates	32k	12 repos	~4.5k	Automated safety check: Notes	MIT	today
Biopythondavila7/claude-code-templates	32k	13 repos	~3.4k	Automated safety check: Pass	MIT	today

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Questions about Ncbi Datasets

What does Ncbi Datasets do?

Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools. Ncbi Datasets is an agent skill from ClawBio/ClawBio. Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

When should I use Ncbi Datasets?

Ncbi Datasets fits situations like: tasks that involve Bioinformatics.

How do I install Ncbi Datasets in Claude Code?

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

How do I install Ncbi Datasets in Codex?

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

Can I use Ncbi Datasets 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 ClawBio/ClawBio --skill ncbi-datasets -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/ncbi-datasets, .gemini/skills/ncbi-datasets, .github/skills/ncbi-datasets and .opencode/skills/ncbi-datasets in your project.

What does Ncbi Datasets need to run?

Going by SKILL.md and its folder, Ncbi Datasets needs the command-line tools its instructions call (conda).

Does Ncbi Datasets access the network?

SKILL.md names 2 domains. As links in the text: ncbi.nlm.nih.gov and doi.org. This is read from the text; nothing was executed.

Is Ncbi Datasets 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 Ncbi Datasets use?

Ncbi Datasets is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Ncbi Datasets use?

About 2.8k tokens (SKILL.md is roughly 11k 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 3.7k tokens, read only when the agent opens those files.

What are the alternatives to Ncbi Datasets?

Skills that share tags, products or a category with Ncbi Datasets: 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 Ncbi Datasets?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 7, 2026.

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

Install Ncbi Datasets

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At a glance

What it does

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Runs code

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SKILL.md

🦖 Skill Name

Trigger

Why This Exists

Core Capabilities

Scope

Workflow

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CLI Reference

Demo

Downloaded ZIP file structure

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Files

Used in 1 other repository

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