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FracSim

Conda PyPI Python 3.8+ License: MIT

FracSim is a fast, memory-efficient command-line tool for estimating bacterial genome similarity using the FracMinHash sketching algorithm. It computes both Jaccard index and Average Nucleotide Identity (ANI) between genomes, enabling large-scale comparative genomics studies.

✨ Key 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.hosted on GitHub.

🚀 Quick Example

Compare two E. coli genomes:

fracsim -i ecoli_k12.fasta ecoli_o157.fasta -k 31 -s 0.01 --ani