ChromDetect Example Data

This directory contains synthetic genome assemblies for testing and demonstration purposes.

Included Files

synthetic_assembly.fasta

A small (~5 KB) synthetic assembly demonstrating various scaffold naming conventions:

Scaffold	Type	Naming Convention
chr1	Chromosome	Explicit chromosome
chr2	Chromosome	Explicit chromosome
chrX	Sex chromosome	Explicit chromosome
chrMT	Mitochondrial	Explicit chromosome
Super_scaffold_1	Chromosome	VGP-style
HiC_scaffold_1	Chromosome	Hi-C scaffolder
LG1	Chromosome	Linkage group
NC_000001.11	Chromosome	NCBI RefSeq
scaffold_1_RaGOO	Chromosome	RaGOO scaffolder
chr1_random	Unlocalized	Random scaffold
chrUn_scaffold1	Unplaced	Unknown chromosome
contig_001	Unplaced	Contig
scaffold_arrow_1	Unplaced	Arrow-polished

synthetic_assembly_v2.fasta

An "improved" version of the assembly for testing comparison mode:

• chr1: Extended
• chr2: Extended
• chrX: Extended
• chr3: New chromosome added
• Some small scaffolds removed (merged)

Quick Start

# Basic analysis
chromdetect examples/synthetic_assembly.fasta

# Compare the two versions
chromdetect examples/synthetic_assembly.fasta --compare examples/synthetic_assembly_v2.fasta

# Generate HTML report
chromdetect examples/synthetic_assembly.fasta --format html -o report.html

# Expected karyotype (10 chromosomes)
chromdetect examples/synthetic_assembly.fasta --karyotype 10

Expected Output

Running chromdetect examples/synthetic_assembly.fasta should show:

• Chromosomes detected: 9 (chr1, chr2, chrX, chrMT, Super_scaffold_1, HiC_scaffold_1, LG1, NC_000001.11, scaffold_1_RaGOO)
• Unlocalized: 2 (chr1_random, chrUn_scaffold1)
• Unplaced: 2 (contig_001, scaffold_arrow_1)

Real-World Test Data

For testing with real genome assemblies, see the main README for download instructions for:

• Saccharomyces cerevisiae S288C (~12 Mb) - Yeast reference genome
• Caenorhabditis elegans (~100 Mb) - Nematode reference genome
• Arabidopsis thaliana (~135 Mb) - Plant reference genome