GENPAT (Italian National Reference Centre for WGS of microbial pathogens)

Ultra-fast SNP/indel-level distance calculator for core and whole genome MLST (cg/wgMLST) analysis in bacterial genomics

Project based on GrapeTree, a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata.

Self-hostable AI platform that generates Nextflow DSL2 pipelines for the cohesive-ngsmanager framework

High-performance pairwise Hamming distance calculator for cgMLST data with GPU acceleration

Genome-anchored calibration of a continuous phenotype across cohorts, with uncertainty-propagated probabilistic labels

Geometry-guided band-doubling for the minimap2 gap-filling DP (faster at identical variant-calling F1; composes with mm2-fast)

Reproducibility material (scripts, data manifests, seeds) for the mm2-geo paper

Fast Rust port of GrapeTree's tree/distance engine (experimental)

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

Trajectory-based long-read aligner with DP-free CIGAR generation