FracSim:fast bacterial genome similarity estimation using FracMinHash sketching
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 .
1 maintainer
Metadata
1 maintainer
Release files for FracSim 1.0.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| fracsim-1.0.2.tar.gz | 20.4 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| fracsim-1.0.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 47.5 kB
Release files / fracsim-1.0.2.tar.gz
| Download URL | fracsim-1.0.2.tar.gz |
|---|---|
| Size | 20.4 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.13.12
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Release files / fracsim-1.0.2-py3-none-any.whl
| Download URL | fracsim-1.0.2-py3-none-any.whl |
|---|---|
| Size | 27.1 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.13.12
|
Security for FracSim 1.0.2
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