bioinformatics

Indexes and fetches 400+ bioinformatics reference skills and runnable pipelines from bioSkills and ClawBio repositories.

Updated Jun 5, 2026
One-click install
npx skills add https://github.com/xu1713/openhorse --skill bioinformatics-xu1713
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: bioinformatics
Source: https://github.com/xu1713/openhorse/tree/main/openhorse/openhorse/optional-skills/research/bioinformatics
Command: npx skills add https://github.com/xu1713/openhorse --skill bioinformatics-xu1713

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? Bioinformatics work spans hundreds of specialized domains, and no single skill can bundle correct parameters, tool flags, and validated pipelines for all of them. This gateway indexes two open-source skill libraries so you can fetch exactly the domain guidance you need on demand instead of guessing tool configurations. ## Core Features & Use Cases - On-demand skill fetching: Shallow-clone the bioSkills (385 reference guides) or ClawBio (33 runnable pipelines) repositories and read the specific skill for your task. - Broad domain coverage: Genomics, variant calling, bulk and single-cell RNA-seq, spatial transcriptomics, epigenomics, metagenomics, pharmacogenomics, structural biology, proteomics, CRISPR screens, and more. - Executable pipelines: ClawBio skills include Python scripts with demo flags and export reproducibility bundles (report.md, commands.sh, environment.yml). - Use Case: You need to annotate a VCF file with clinical significance. Fetch the ClawBio vcf-annotator skill to run VEP + ClinVar + gnomAD annotation, or read the bioSkills variant-annotation guide for correct parameters. ## Quick Start Ask the assistant to fetch the appropriate bioinformatics skill for your task, for example: clone the bioSkills repo and show me the GATK variant calling guide.

Frequently Asked Questions about bioinformatics

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

FAQPage Schema
How do I use bioinformatics skills from bioSkills and ClawBio?

Shallow-clone the relevant repository with git clone --depth 1, then read the specific skill file for your domain. bioSkills skills live at <category>/<skill-name>/SKILL.md as reference guides, while ClawBio skills live at skills/<skill-name>/ with runnable Python scripts.

What is the difference between bioSkills and ClawBio?

bioSkills provides 385 reference guides with code patterns, correct parameters, and decision trees, but they are not executable pipelines. ClawBio provides 33 runnable pipeline skills with Python scripts, demo flags, and reproducibility bundles including environment.yml files.

Does this skill work on macOS and Linux?

Yes, the skill supports both Linux and macOS platforms. CLI tools like samtools, bcftools, and minimap2 can be installed via apt on Ubuntu, Homebrew on macOS, or through Bioconda for reproducible environments.

Can I run variant calling or RNA-seq pipelines directly?

ClawBio pipelines such as rnaseq-de and vcf-annotator are executable and many support --demo flags after running pip install -r requirements.txt. bioSkills entries are reference material only, so you follow their code patterns manually rather than executing them.

What are the limitations of this bioinformatics gateway?

The fetched skills are not in Hermes SKILL.md format and must be treated as expert reference material. Both repos assume bioinformatics tools are preinstalled, and genomic data files like reference genomes or SRA datasets can require substantial disk space.