UKDRI Bioinformatics Toolkit

A comprehensive Quarto-based website for onboarding students to bioinformatics, with a focus on genomics and dementia research.

What's Included

This toolkit contains:

1. Homepage (index.qmd) - Welcome page with getting started guide
2. Tools & Setup (tools-setup.qmd) - Essential genomics tools with installation instructions
3. Genomics Fundamentals (genomics-fundamentals.qmd) - Core concepts for dementia research
4. Tutorials & Workshops (tutorials-workshops.qmd) - Comprehensive course catalogue
5. Best Practices (best-practices.qmd) - Analysis catalogue template, folder structure, documentation guide
6. Resources (resources.qmd) - Databases, communities, and learning resources

File Structure

ukdri-bioinformatics-toolkit/
├── _quarto.yml              # Configuration file
├── custom.scss              # UKDRI color theme
├── styles.css               # Additional styling
├── index.qmd                # Homepage
├── tools-setup.qmd          # Tools & Setup page
├── genomics-fundamentals.qmd # Genomics Fundamentals page
├── tutorials-workshops.qmd   # Tutorials & Workshops page
├── best-practices.qmd        # Best Practices page
└── resources.qmd             # Resources page

Customization

Update Colors

Edit custom.scss to change the color scheme:

$primary: #1e3a8a;       // Deep blue
$secondary: #7c3aed;     // Purple
$accent: #ec4899;        // Pink/magenta

Key Features for Students

Analysis Catalogue Template

Located in best-practices.qmd - a comprehensive template for tracking all analyses with fields for:

• Analysis ID, dates, project name
• Input data, sample size
• Scripts, software versions
• Key parameters and findings
• Issues and follow-up needed

Folder Structure Generator

Bash script in best-practices.qmd that creates standardized project directories:

• Organized data/scripts/results structure
• Git-ready with .gitignore
• README templates
• Preserves raw data integrity

Tool Descriptions

Each tool in tools-setup.qmd includes:

• What it does (plain language)
• Use cases
• Installation instructions
• Basic usage examples

Comprehensive Tutorial List

tutorials-workshops.qmd contains 40+ courses organized by:

• Genomics & NGS
• Population genetics
• Workflows (Snakemake, Nextflow)
• Programming (Python, R)
• HPC and containers
• All with direct links and descriptions

Tips for Use

• Browser Search: Use Ctrl/Cmd+F to search within pages
• Copy Code: Hover over code blocks to see copy button
• Mobile Friendly: Responsive design works on phones/tablets
• Printable: Print-friendly styles included

Created: October 2025

ukdri-bioinformatics-toolkit