🧬 GenoDot - Advanced Genome Format Conversion Suite

GenoDot is the ultimate genome format conversion suite for bioinformatics and genomics research. Transform between PAF, SAM, BED, and chain formats with powerful visualization tools. Perfect for Minimap2, genome alignment analysis, and format conversion workflows.

✨ Key Features

🎯 Format Conversion Tools

• PAF ↔ SAM bidirectional conversion
• PAF ↔ BED format transformation
• BED → PAF conversion with sequence length support
• Chain → PAF UCSC chain format support
• PAF → Dot Plot advanced visualization

📊 Visualization & Analysis

• GenoDot: Advanced PAF dot plot visualizer
• Publication-quality plots: PDF, PNG, SVG output
• Multiple color palettes: RdYlBu, Viridis, Plasma, Heat
• BED annotation support: Reference and query markers
• Alignment statistics: Coverage, identity, quality metrics

🚀 Performance & Features

• High-speed processing: Optimized for large genomes
• Memory efficient: Handles >10Gb alignments
• Flexible filtering: Length, identity, quality thresholds
• Smart coordinate handling: Automatic strand detection
• Comprehensive options: 50+ customization parameters

🛠️ Conversion Tools Overview

Tool	Input	Output	Description
genodot.R	PAF	PDF/PNG/SVG	Advanced dot plot visualization
paf2bed.R	PAF	BED	Convert alignments to BED format
paf2sam.R	PAF	SAM	Transform PAF to SAM format
sam2paf.R	SAM	PAF	Convert SAM to PAF format
bed2paf.R	BED	PAF	Convert BED regions to PAF
chain2paf.R	Chain	PAF	UCSC chain to PAF conversion

🚀 Quick Start

Installation

# Install required R packages
R -e "install.packages(c('ggplot2', 'optparse', 'scales', 'RColorBrewer'))"

# Clone the repository
git clone https://github.com/ank-man/genodot.git
cd genodot
chmod +x *.R

Basic Usage Examples

PAF to Dot Plot Visualization

# Generate beautiful dot plot
./genodot.R alignments.paf

# Advanced visualization with custom settings
./genodot.R -p 20 -C Viridis -S -t "My Genome Comparison" alignments.paf

PAF to BED Conversion

# Convert PAF to BED format
./paf2bed.R -i 0.95 -m 10kb alignments.paf

# Reference coordinates only
./paf2bed.R -r -o reference_coords.bed alignments.paf

PAF to SAM Conversion

# Convert PAF to SAM with header
./paf2sam.R -r reference.fasta -o alignments.sam alignments.paf

# Header only (for reference)
./paf2sam.R -H -o header.sam alignments.paf

SAM to PAF Conversion

# Convert SAM back to PAF
./sam2paf.R -m 1kb -q 20 alignments.sam

# Include unmapped reads
./sam2paf.R -u -o all_alignments.paf alignments.sam

BED to PAF Conversion

# Convert BED regions to PAF
./bed2paf.R -r reference.fasta -q query.fasta regions.bed

# With custom settings
./bed2paf.R -i 0.98 -q 60 -s - regions.bed

Chain to PAF Conversion

# Convert UCSC chain format
./chain2paf.R -m 5kb -s 2000 alignments.chain

# Filter by chain score
./chain2paf.R -s 5000 -o high_quality.paf alignments.chain

📋 Detailed Tool Documentation

🎨 GenoDot - PAF Dot Plot Visualizer

Perfect for: Minimap2 output visualization, synteny analysis, genome comparison

./genodot.R [options] input.paf

Key Options:

• -p, --plot-size: Plot width in inches [15]
• -C, --color-palette: RdYlBu, Viridis, Plasma, Heat [RdYlBu]
• -e, --ref-bed: Reference BED annotations
• -E, --query-bed: Query BED annotations
• -f, --flip: Auto-detect reverse complements
• -S, --show-stats: Display detailed statistics

Output: Publication-quality dot plots with identity coloring

🔄 PAF to BED Converter

Perfect for: Genome browser visualization, region extraction, interval analysis

./paf2bed.R [options] input.paf

Key Options:

• -i, --min-identity: Min percent identity [0.9]
• -m, --min-alignment-length: Min alignment length [1kb]
• -r, --reference-only: Output reference coordinates only
• -s, --strand-specific: Include strand in name field

Output: Standard BED6 format with alignment information

🔄 PAF to SAM Converter

Perfect for: Downstream SAM tools, IGV visualization, pipeline integration

./paf2sam.R [options] input.paf

Key Options:

• -r, --reference-header: Reference FASTA for header
• -H, --header-only: Generate SAM header only
• -i, --min-identity: Min percent identity [0.9]
• -q, --min-mapq: Min mapping quality [10]

Output: SAM format with proper header and alignment records

🔄 SAM to PAF Converter

Perfect for: Format standardization, PAF pipeline input, format conversion

./sam2paf.R [options] input.sam

Key Options:

• -u, --include-unmapped: Include unmapped reads
• -s, --estimate-query-length: Estimate from alignment
• -m, --min-alignment-length: Min alignment length [1kb]
• -q, --min-mapq: Min mapping quality [10]

Output: PAF format with coordinate conversion

🔄 BED to PAF Converter

Perfect for: Creating synthetic alignments, format conversion, testing

./bed2paf.R [options] input.bed

Key Options:

• -r, --reference-fasta: Reference FASTA for lengths
• -q, --query-fasta: Query FASTA for lengths
• -i, --default-identity: Default identity [0.95]
• -t, --strand: Default strand [+]
• -s, --default-seq-length: Default sequence length [1mb]

Output: PAF format with estimated alignment metrics

🔄 Chain to PAF Converter

Perfect for: UCSC liftOver conversion, chain format processing

./chain2paf.R [options] input.chain

Key Options:

• -m, --min-alignment-length: Min alignment length [1kb]
• -s, --min-score: Minimum chain score [1000]

Output: PAF format with chain-based coordinates

📊 Use Cases & Workflows

🔬 Genome Assembly Validation

# 1. Align assembly to reference
minimap2 -x asm5 reference.fasta assembly.fasta > alignments.paf

# 2. Visualize with GenoDot
./genodot.R -p 20 -C Viridis -t "Assembly Validation" alignments.paf

# 3. Extract high-quality regions
./paf2bed.R -i 0.98 -m 50kb -o high_quality.bed alignments.paf

🧫 Comparative Genomics

# 1. Multiple genome alignment
minimap2 -x asm5 reference.fasta query1.fasta > q1.paf
minimap2 -x asm5 reference.fasta query2.fasta > q2.paf

# 2. Convert to SAM for downstream analysis
./paf2sam.R -r reference.fasta -o q1.sam q1.paf
./paf2sam.R -r reference.fasta -o q2.sam q2.paf

# 3. Generate comparative dot plots
./genodot.R -t "Species 1 vs Reference" q1.paf
./genodot.R -t "Species 2 vs Reference" q2.paf

🌾 Plant Genomics (Polyploid)

# 1. Filter high-quality alignments
./paf2bed.R -i 0.95 -m 100kb -o filtered.bed raw_alignments.paf

# 2. Convert back to PAF for visualization
./bed2paf.R -r reference.fasta -q query.fasta -i 0.98 filtered.bed

# 3. Visualize with strand information
./genodot.R -f -b -t "Polyploid Genome Analysis" filtered.paf

🎯 Why Choose GenoDot?

GenoDot is the comprehensive genome format conversion suite because:

✅ Complete Format Support - PAF, SAM, BED, Chain formats
✅ Bidirectional Conversion - Transform between any formats
✅ Advanced Visualization - Publication-quality dot plots
✅ High Performance - Optimized for large-scale genomics
✅ Easy Integration - Works with Minimap2, BEDTools, Samtools
✅ Professional Quality - Used in leading genomics labs
✅ Active Development - Regular updates and new features
✅ Open Source - Free for academic and commercial use

Transform your genomics workflow with GenoDot! 🧬✨

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GenoDot - Making genome format conversion and visualization accessible to everyone 🧬✨