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FracSim:fast bacterial genome similarity estimation using FracMinHash sketching

Latest Version PyPI version Python 3.8+ Platform License: MIT

FracSim is a fast and accurate tool for estimating bacterial genome similarity, based on the FracMinHash genome sketching algorithm. It compresses large genomes into compact hash sets to rapidly compute Jaccard similarity and ANI (Average Nucleotide Identity) between genomes.

Whether for species identification, strain typing, or large-scale genome comparison, FracSim significantly reduces memory usage and computation time while maintaining high accuracy.

Documents: https://zhuyu534.github.io/FracSim

✨ Features

  • Fast: Uses FracMinHash sketching to dramatically lower memory footprint and runtime.
  • Accurate: Provides Jaccard index and ANI (Average Nucleotide Identity) estimates.
  • Flexible: Supports FASTA/Q formats, configurable k‑mer size and sampling rate.
  • Easy to use: Clean command‑line interface with multi‑threading support.
  • Open source: MIT licensed – contributions and usage are welcome.

📦 Installation

Requirements

  • Python 3.8 or higher

Method 1: Download binaries

Check out the Download Page for pre-built binaries across all supported platforms.

Method 2: Install From PyPI

pip install FracSim

Method 3: Install from source

git clone https://github.com/zhuyu534/FracSim.git
cd FracSim
pip install -e .