chewbbaca

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tripitakit / mlst2dist

mlst2dist.py computes a distance matrix from a chewBBACA MLST alleles table, using Hamming Distance modified with correction for missing data

genomics mlst distance-calculation hamming-distance cgmlst distance-matrix wgmlst dissimilarity-matrix chewbbaca

Updated Apr 19, 2022
Python

cinnetcrash / Lgarvieae-cgMLST

Star

Core genome MLST schema for Lactococcus garvieae (chewBBACA-compatible, 1100 loci, built from 247 QC'd genomes)

mlst cgmlst aquaculture genomic-epidemiology chewbbaca bacterial-typing lactococcus-garvieae

Updated Aug 3, 2026
HTML

andreaderuvo / cgmlst-hamming-gpu

Star

Exact cgMLST allelic (Hamming) distance matrices on the GPU for bacterial genomic epidemiology: 63k profiles in seconds using 1-bit tensor cores, no approximation

rust bioinformatics gpu cuda mlst hamming-distance cgmlst distance-matrix outbreak-detection tensor-cores genomic-epidemiology chewbbaca bacterial-genomics

Updated Nov 3, 2026
Cuda

genpat-it / cgmlst-dists-rs

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Ultra-fast SIMD (AVX-512) pairwise cgMLST Hamming distance matrix — Rust reimplementation of cgmlst-dists-py, byte-identical output, ~6x faster than the C cgmlst-dists

rust bioinformatics genomics simd mlst hamming-distance cgmlst genomic-surveillance chewbbaca

Updated Nov 3, 2026
Rust

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