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MubasherMohammed
MubasherMohammedCOMMUNITY
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ncbi-datasets

Download NCBI genomic, gene, virus, and taxonomy data via CLI tools.

Updated May 10, 2026
Search Tags:#bioinformatics#genomics#taxonomy#ncbi#gene#virus
One-click install
npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill ncbi-datasets-mubashermohammed
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ncbi-datasets
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/ncbi-datasets
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill ncbi-datasets-mubashermohammed

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires datasets, dataformat, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the retrieval of bioinformatics data from NCBI, allowing users to download genomes, genes, virus sequences, and taxonomy data efficiently.

Core Features & Use Cases

  • Download Genomes, Genes, Viruses, and Taxonomy Data: Automatically download various types of data from NCBI using the datasets and dataformat CLI tools.
  • Use Case: Quickly download reference genomes, gene sequences, or virus sequences by providing specific accession numbers, gene symbols, or taxon IDs.
  • Data Retrieval by Filters: Retrieve data with specific filters such as assembly source, release date, or reference status.

Quick Start

Use the ncbi-datasets skill to download the genome data for 'GCF_000001405.40' and save it as 'human_genome.zip'.

Frequently Asked Questions about ncbi-datasets

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I download reference genomes from NCBI by accession number?▼

The skill automates downloading genomic data from NCBI by accepting specific accession numbers as input and saving the fetched biological sequences as a zip file. It leverages the datasets CLI tool for efficient retrieval of reference genomes.

Can I filter NCBI genomic data by assembly source or release date?▼

Yes, the skill supports retrieving data with specific filters such as assembly source, release date, or reference status. This functionality enables you to narrow down the genomic, gene, or virus sequences downloaded from NCBI to match your specific research criteria.

Do I need to install any tools to retrieve virus sequences and taxonomy data?▼

Yes, the datasets and dataformat CLI tools must be installed and configured on your system. These dependencies are strictly required to automate the download and retrieval of virus sequences and taxonomy data from NCBI.

What is the best way to retrieve gene sequences using a taxon ID?▼

By providing specific taxon IDs or gene symbols as input, you can automate the download of gene sequences from NCBI. This approach uses the datasets CLI to fetch targeted bioinformatics data quickly without requiring manual web navigation.

How do I extract and format downloaded bioinformatics data from NCBI?▼

The dataformat CLI tool processes the downloaded biological datasets, allowing you to extract and format the genomic, gene, or virus data retrieved by the datasets tool. This ensures the output is properly structured for downstream analysis.

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