clustkit 0.1.1

Accurate protein sequence clustering via LSH, Smith-Waterman alignment, and Leiden community detection

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ClustKIT is a bioinformatics tool for protein sequence clustering. It combines MinHash sketching, locality-sensitive hashing (LSH), banded Smith-Waterman alignment with BLOSUM62 scoring, and Leiden community detection to achieve high clustering accuracy at all identity thresholds, including the challenging low-identity regime (30-50%) where greedy heuristic methods lose sensitivity.

Features

• Accurate at low identity: Smith-Waterman alignment with BLOSUM62 scoring and Leiden graph partitioning produce well-connected clusters, especially at thresholds below 50%
• Fast: Multi-stage filtering (LSH + Jaccard pre-filter + length-ratio filter) eliminates >98% of candidate pairs before alignment
• Scalable: C/OpenMP alignment kernel with configurable thread count; optional GPU acceleration via CuPy
• Flexible clustering: Leiden community detection (default), connected components, or greedy

Installation

pip install clustkit

With GPU acceleration (requires CUDA 12.x):

pip install clustkit[gpu]

From source:

git clone https://github.com/JLSteenwyk/ClustKIT.git
cd ClustKIT
pip install -e ".[dev]"

Quick start

# Cluster proteins at 50% identity using 8 threads
clustkit -i proteins.fasta -o output/ -t 0.5 --threads 8

# Use connected components instead of Leiden
clustkit -i proteins.fasta -o output/ -t 0.7 --cluster-method connected --threads 4

# GPU-accelerated alignment
clustkit -i proteins.fasta -o output/ -t 0.3 --device 0 --threads 8

Output files:

• output/clusters.tsv — Cluster assignments (sequence_id, cluster_id, is_representative)
• output/representatives.fasta — Representative sequences
• output/run_info.json — Run parameters and statistics

Pipeline overview

ClustKIT clusters sequences through six phases:

1. Read — Parse FASTA/FASTQ, integer-encode sequences
2. Sketch — MinHash bottom-s sketches with adaptive k-mer size
3. LSH — Locality-sensitive hashing to find candidate pairs
4. Align — Banded Smith-Waterman with BLOSUM62 scoring, affine gap penalties, length-ratio and Jaccard pre-filters
5. Graph — Sparse similarity graph construction
6. Cluster — Leiden community detection (default), connected components, or greedy

CLI reference

clustkit   Cluster sequences by identity threshold

Options

Option	Description	Default
-i, --input	Input FASTA/FASTQ file	required
-o, --output	Output directory	required
-t, --threshold	Identity threshold (0.0-1.0)	0.9
--threads	Number of CPU threads	1
--device	cpu, auto, or GPU device ID (e.g., 0)	cpu
--cluster-method	leiden (default), connected, or greedy	leiden
--alignment	align (SW, accurate) or kmer (fast)	align
--clustering-mode	Presets: balanced, accurate, or fast	balanced
--sensitivity	LSH sensitivity: low, medium, high	per mode
--sketch-size	MinHash sketch size	128
-k, --kmer-size	K-mer size for sketching	5
--representative	longest, centroid, or most_connected	longest
--format	Output format: tsv or cdhit	tsv

Dependencies

Core (installed automatically):

Package	Purpose
numpy	Array operations
numba	JIT-compiled fallback kernels
biopython	FASTA/FASTQ parsing
scipy	Sparse graph, connected components
leidenalg	Leiden community detection
python-igraph	Graph representation for Leiden
typer + rich	CLI framework

Optional:

Package	Install	Purpose
cupy-cuda12x	pip install clustkit[gpu]	GPU-accelerated Smith-Waterman alignment

License

MIT License. See LICENSE for details.