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bioinformatics

Index and fetch bioinformatics reference skills and runnable pipelines.

Updated Mar 25, 2026
Search Tags:#reference#bioinformatics#genomics#pipelines#variant-calling#skill-gateway
One-click install
npx skills add https://github.com/afel6/scal-ai-pipeline --skill bioinformatics-afel6
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bioinformatics
Source: https://github.com/afel6/scal-ai-pipeline/tree/main/hermes_skills_library/optional-skills/research/bioinformatics
Command: npx skills add https://github.com/afel6/scal-ai-pipeline --skill bioinformatics-afel6

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill provides a single discovery and retrieval interface for hundreds of domain-specific bioinformatics reference guides and runnable pipelines, removing the need to manually search multiple repositories and documentation sources.

Core Features & Use Cases

  • Indexed Discovery: Maps and indexes bioSkills reference topics and ClawBio runnable pipelines for rapid lookup across genomics, transcriptomics, single-cell, metagenomics, structural biology, and clinical genomics domains.
  • On-demand Fetching: Performs shallow clones of external repositories and reads skill README or SKILL.md files to extract parameters, required tools, environment specifications, and example commands.
  • Use Case: Quickly locate a GATK variant-calling guide, extract recommended flags and preprocessing steps, and obtain the ClawBio pipeline location and environment requirements for execution.

Quick Start

Clone the bioSkills and ClawBio repositories and ask for a concise summary of the specific skill's required tools, key commands, and expected outputs.

Frequently Asked Questions about bioinformatics

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

FAQPage Schema
How do I find bioinformatics pipelines and reference guides for genomics analysis?▼

Bioinformatics pipelines and reference guides are discovered through an indexed interface mapping 400+ domain-specific skills across genomics, transcriptomics, and metagenomics for rapid lookup and retrieval.

What's the best way to locate a GATK variant-calling guide and its required environment parameters?▼

To locate a GATK variant-calling guide, fetch the specific bioinformatics skill on demand to extract recommended flags, preprocessing steps, required tools, and environment specifications directly from the documentation.

Can I retrieve single-cell RNA sequencing workflows without manually searching multiple repositories?▼

Single-cell RNA sequencing workflows can be retrieved without manual repository searches by using the indexed discovery feature to shallow clone external sources and read the relevant documentation directly.

Does this bioinformatics gateway support reproducible workflows for clinical genomics and pharmacogenomics?▼

The bioinformatics gateway supports reproducible workflows for clinical genomics and pharmacogenomics by indexing runnable pipelines and delivering summarized parameters alongside execution guidance.

How do I get summarized tool requirements and example commands for a metagenomics pipeline?▼

To get summarized tool requirements and example commands for a metagenomics pipeline, trigger an on-demand fetch to read the SKILL.md or README files and extract the necessary execution details.

What bioinformatics domains are covered by the indexed reference skills for transcriptomics and structural biology?▼

Indexed reference skills cover transcriptomics and structural biology alongside genomics, single-cell analysis, variant calling, metagenomics, and pharmacogenomics for research and analysis scenarios.

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