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bioinformatics

Match genomics tasks to indexed bioSkills references and ClawBio pipelines.

Updated May 26, 2026
Search Tags:#bioinformatics#genomics#pharmacogenomics#sequencing#metagenomics#variant calling#single-cell rna-seq
One-click install
npx skills add https://github.com/ruiyangruiyi/hermes-agent --skill bioinformatics-ruiyangruiyi
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bioinformatics
Source: https://github.com/ruiyangruiyi/hermes-agent/tree/main/optional-skills/research/bioinformatics
Command: npx skills add https://github.com/ruiyangruiyi/hermes-agent --skill bioinformatics-ruiyangruiyi

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Bioinformatics workflows often require locating correct, tool-specific parameters and domain knowledge scattered across many repositories, which makes it slow and error-prone to start the right analysis.

Core Features & Use Cases

  • Gateway indexing across bioSkills and ClawBio: Selects a domain topic and skill name from a curated index covering genomics, transcriptomics, single-cell, variants, pharmacogenomics, metagenomics, structural biology, and more.
  • On-demand reference fetching: Clones the needed repository(s) and directs you to the exact topic-level guide or runnable pipeline materials.
  • Correct “how to use it” expectations: Ensures you treat bioSkills as reference guides (parameter/decision support) and ClawBio as executable pipeline skill materials (scripts and reproducibility artifacts).

Use case example: You need a parameter-accurate walkthrough for variant calling and want to quickly find a vetted reference for the relevant method, or a runnable pipeline with an environment and demo artifacts if available.

Quick Start

Ask for a skill by domain and task, for example: “Fetch and summarize the bioinformatics reference for gatk-variant-calling, then explain the recommended inputs, key parameters to verify, and how to validate the output quality.”

Frequently Asked Questions about bioinformatics

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

FAQPage Schema
How do I find the right parameters for variant calling and annotation pipelines?▼

To find parameters for variant calling, this skill matches your task to indexed bioSkills reference topics, fetching vetted guides for correct, tool-specific inputs and decision support. It clones the needed repository to provide parameter-accurate walkthroughs for your analysis.

What is the best way to locate a runnable pipeline for single-cell RNA-seq analysis?▼

For single-cell RNA-seq, the skill retrieves ClawBio runnable pipeline packages by matching your task to a curated index. It directs you to executable pipeline materials, scripts, and reproducibility artifacts rather than just static documentation.

Does this bioinformatics skill execute metagenomics workflows directly?▼

No, the bioinformatics skill does not execute workflows directly. It clones upstream libraries on demand and provides their SKILL.md/README documentation as expert reference material for metagenomics tasks, functioning as a guide rather than a native executable environment.

Can I use this for pharmacogenomics and epigenomics task guidance?▼

Yes, you can use this for pharmacogenomics and epigenomics. It indexes domains across genomics, transcriptomics, variants, and structural biology, fetching the exact topic-level guide needed to verify inputs and validate output quality for these specific tasks.

How do I get a vetted reference for sequence QC and alignment?▼

Ask for a skill by domain and task to get a sequence QC and alignment reference. The skill selects a domain topic from a curated index, clones the required repository, and summarizes the bioinformatics reference including recommended inputs and key parameters.

What are the limitations of using indexed repositories for differential expression analysis?▼

A limitation is that you must treat bioSkills as reference guides and ClawBio as executable pipeline materials. It requires cloning upstream libraries on demand, meaning you rely on external repository documentation rather than Hermes-native executable skills for differential expression.

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