BSR-Based Allele Calling Algorithm
🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
Fast cgMLST/wgMLST allele caller with SIMD Smith-Waterman scoring (parasail) and an offline schema-side minimizer-overlap audit. 10.7–22.3× faster than chewBBACA with 100% DNA-sequence agreement on bilaterally callable cells.
A Platform for Epidemiological Investigation and Comparative Genomic Analysis
mlst2dist.py computes a distance matrix from a chewBBACA MLST alleles table, using Hamming Distance modified with correction for missing data
Genome-anchored calibration of a continuous phenotype across cohorts, with uncertainty-propagated probabilistic labels
Information-theoretic gene-content and allele-type dependency discovery for bacterial WGS (research preview)
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