chromdetect 0.6.0

Detect chromosome-level scaffolds in genome assemblies with inconsistent naming conventions

ChromDetect

A toolkit for genome assembly classification, validation, and quality control.

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Overview

ChromDetect helps you work with genome assemblies by providing six key capabilities:

Feature	Description
Scaffold Classification	Identify chromosomes vs unplaced scaffolds based on naming patterns and size
Assembly Validation	Validate FASTA files against NCBI assembly reports
Karyotype Checking	Verify chromosome counts against 29 species databases
Name Standardization	Convert between UCSC, Ensembl, RefSeq, and GenBank conventions
Version Tracking	Compare assembly versions and detect scaffold changes
QC Dashboard	Generate comparative reports across multiple assemblies

Installation

pip install chromdetect

Quick Examples

# Classify scaffolds in an assembly
chromdetect assembly.fasta

# Validate against NCBI report
chromdetect assembly.fasta --assembly-report report.txt --validate

# Check chromosome count for human
chromdetect assembly.fasta --check-karyotype human

# Convert to UCSC naming (chr1, chr2, chrX)
chromdetect assembly.fasta --rename ucsc -o renamed.fasta

# Compare two assembly versions
chromdetect v1.fasta --compare-versions v2.fasta

# Generate QC dashboard for multiple assemblies
chromdetect --dashboard *.fasta -o dashboard.html --format html

Use Cases

Preparing assemblies for submission

Before submitting to NCBI, check compliance and standardize names:

# Check if names meet NCBI requirements
chromdetect assembly.fasta --check-compliance

# Rename to standard convention
chromdetect assembly.fasta --rename refseq -o submission_ready.fasta

Quality control across projects

Compare multiple assemblies from different sources:

# Generate comparative dashboard
chromdetect --dashboard sample1.fa sample2.fa sample3.fa -o qc_report.html --format html

Validating downloaded assemblies

Verify a FASTA matches its NCBI assembly report:

chromdetect GRCh38.fasta --assembly-report GRCh38_report.txt --validate --strict

Tracking assembly improvements

See what changed between versions:

chromdetect old_assembly.fasta --compare-versions new_assembly.fasta

Output shows promotions, demotions, and metric changes:

SCAFFOLD CHANGES:
  Promoted:    2 scaffolds (unplaced → chromosome)
  Unchanged:   1,150 scaffolds
  N50 change:  +6.7 Mb (+14.6%)

Checking species-specific karyotype

Verify your assembly has the expected chromosomes:

# List available species
chromdetect --list-species

# Check against expected karyotype
chromdetect mouse_assembly.fasta --check-karyotype mouse

Output Formats

Format	Flag	Use Case
Summary	--format summary	Quick terminal inspection (default)
JSON	--format json	Programmatic processing
TSV	--format tsv	Spreadsheet analysis
HTML	--format html	Visual reports with charts
BED	--format bed	Genomics pipelines (bedtools, etc.)
GFF	--format gff	Genome browsers

Python API

from chromdetect import classify_fasta

# Classify an assembly
results, stats = classify_fasta("assembly.fasta")
print(f"Chromosomes: {stats.chromosome_count}")
print(f"N50: {stats.n50 / 1e6:.1f} Mb")

# Filter to just chromosomes
chromosomes = [r for r in results if r.classification == "chromosome"]
for c in chromosomes:
    print(f"  {c.name}: {c.length:,} bp")

Additional modules for specific tasks:

# Validation
from chromdetect.validation import validate_fasta_against_report

# Karyotype checking
from chromdetect.karyotype import validate_karyotype, KaryotypeDatabase

# Name standardization
from chromdetect.standardize import standardize_fasta, check_ncbi_compliance

# Version comparison
from chromdetect.version import compare_fasta_files

# Multi-assembly dashboard
from chromdetect.dashboard import analyze_multiple_assemblies, generate_dashboard_html

Supported Species (Karyotype Database)

ChromDetect includes karyotype data for 29 species:

Mammals: Human, mouse, rat, dog, cat, horse, cow, pig, sheep, goat, rabbit, guinea pig

Other vertebrates: Chicken, zebrafish, frog

Invertebrates: Fruit fly, C. elegans

Plants: Arabidopsis, rice, maize, wheat, soybean, tomato

Microorganisms: Yeast (S. cerevisiae), E. coli

Use chromdetect --list-species to see all available species with chromosome counts.

Recognized Naming Patterns

ChromDetect automatically recognizes common scaffold naming conventions:

• Chromosome prefixes: chr1, Chr_1, chromosome_1, Chromosome1
• Super scaffolds: Super_scaffold_1, Superscaffold_1, SUPER_1
• Linkage groups: LG1, LG_1, linkage_group_1
• NCBI accessions: NC_000001.11, CM000663.2
• Assembly tools: HiC_scaffold_1, Scaffold_1_RaGOO
• Simple numeric: 1, 2, X, MT

Custom patterns can be added via YAML configuration files.

Limitations

ChromDetect uses naming patterns and size heuristics—it cannot:

• Detect misassemblies or sequence errors
• Validate sequence correctness
• Perform synteny or homology analysis

For comprehensive assembly validation, use ChromDetect alongside tools like QUAST or Merqury.

Citation

If you use ChromDetect in your research, please cite:

@software{chromdetect,
  author = {Handley, Scott A.},
  title = {ChromDetect: A toolkit for genome assembly classification and QC},
  url = {https://github.com/shandley/chromdetect},
  version = {0.6.0},
  doi = {10.5281/zenodo.17945062},
  year = {2025}
}

License

MIT License - see LICENSE for details.

Contributing

Contributions welcome! See CONTRIBUTING.md for guidelines.