PolyCore

PolyCore is a Python-based tool for core genome analysis in polyploid organisms.
It loads reference and sample FASTA files, collapses identical sequences, filters by genome/core fractions, and produces:

• Core / Full alignment FASTA files
• Pairwise distance matrices (wide and long formats)
• Per-sample summary table
• Progressive core fraction plot (HTML)

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Features

• Handles haploid and polyploid genomes (auto-detects ploidy if not specified)
• Soft-core / progressive core fraction calculation
• Collapsing and re-expansion of identical sequences
• Distance matrices with efficient chunking (auto memory-aware)
• Output in CSV, FASTA, and VCF formats
• Interactive visualization with Plotly

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Installation

Option 1 - Use the container (Preferred Method):

docker pull public.ecr.aws/o8h2f0o1/polycore:1.0.0

Option 2 - Clone the repository and install:

git clone https://github.com/WA-DOH/polycore.git
cd polycore
pip install -e .

PolyCore requires Python 3.10+. Dependencies (numpy, screed, psutil, plotly) are installed automatically.

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Usage

Run PolyCore from the command line:

polycore \
    --progressive \
    --ref reference.fasta \
    sample1.fasta sample2.fasta

Common options

• --min-gf : Minimum genome fraction per sample (default: 0.9)
• --min-cf : Minimum fraction of population required per site (default: 0.95)
• --ploidy : Force ploidy (otherwise auto-detected)
• --progressive : Enable soft-core (progressive) calculation
• --split : Treat each contig in each assembly as a separate sample

For full options:

polycore --help

Outputs

Outputs

• core.aln : Core alignment (variants only, FASTA)
• core.full.aln : Full core alignment (FASTA)
• full.csv : Per-site summary for all passing samples
• dist_wide.csv : Pairwise distance matrix (wide)
• dist_long.csv : Pairwise distance matrix (long/tidy)
• summary.csv : Per-sample statistics
• core_fraction_plot.html : Interactive visualization of soft-core genome fraction