Metadata-Version: 2.4
Name: FracSim
Version: 1.0.0
Summary: a FracMinHash-based genome similarity estimator for bacteria
Home-page: https://github.com/zhuyu534/FracSim.git
Author: YuZhu
Author-email: zhuyu1068@gmail.com
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: mmh3>=4.0.0
Requires-Dist: numpy>=1.21.0
Requires-Dist: pytest>=7.0.0
Requires-Dist: pytest-cov>=4.0.0
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license-file
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## <img src="images/logo.png" width="40" height="40" style="border-radius: 50%; vertical-align: text-bottom; margin-right: 8px;"> FracSim:fast bacterial genome similarity estimation using FracMinHash sketching

[![Latest Version](https://img.shields.io/github/v/release/zhuyu534/FracSim?color=red)](https://github.com/zhuyu534/FracSim/releases)
[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
[![Platform](https://img.shields.io/badge/platform-linux%20%7C%20macos%20%7C%20windows-lightgrey?color=orange)](https://github.com/zhuyu534/FracSim)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

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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
- pip package manager

### Install from source 

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