BaClasT -- Bacterial Classification Tool

Fast classification of assembled bacterial genomes into ESKAPE pathogen species using k-mer frequency profiling.

Install

uv add baclast

CLI

baclast --predict genome.fna
baclast --predict genomes/ -o results.csv

Python

import src.classifier as baclast

baclast.predict(file="genome.fna")
baclast.to_csv(baclast.predict(file="genome.fna"), "results.csv")

What it classifies

ESKAPE pathogens (E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, E. cloacae) plus an "Other" class for non-ESKAPE bacteria. Includes centroid-based out-of-distribution detection.

How it works

Computes 4-mer frequency profiles (256 features) from genome assemblies and classifies with a Random Forest. A bundled pre-trained model is included -- no training data or setup required.

Requirements

Python >= 3.12, biopython, scikit-learn, joblib, numpy.

License

MIT