ncbi-datasets
Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.
npx skills add BioTender-max/awesome-bio-agent-skills --skill ncbi-datasets --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 🦖 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 1. **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 2. **Gene sequence retrieval** — download by NCBI Gene ID, gene symbol, RefSeq accession, locus ta
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Workflow
- Input Formats
- CLI Reference
- Demo
- Downloaded ZIP file structure
- Dependencies
- Error handling
- Safety
- Citations
datasets summary genome taxon human --assembly-source refseq --as-json-lines \ datasets download genome taxon human --reference --include genome,gff3 \ datasets download genome accession GCF_000001405.40 --filename human_GRCh38.zip datasets download gene symbol BRCA1 --taxon human \ datasets download gene gene-id 59272 --ortholog mammals --filename ace2_mammals.zip datasets download virus genome taxon sars-cov-2 --host dog \ datasets download taxonomy taxon 'bos taurus' --include names --parents --children datasets download genome accession --inputfile accessions.txt \ unzip bacteria.zip -d bacteria datasets rehydrate --directory bacteria/ --max-workers 20
What does the ncbi-datasets skill do?
Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill ncbi-datasets --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.