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49 repositories

cgmlst-dists-py
Public
High-performance pairwise Hamming distance calculator for cgMLST data with GPU acceleration
bioinformatics genomics gpu
bioinformatics genomics gpu numpy cuda distance-calculation hamming-distance cgmlst bioinformatics-tool cgmlst-genes
Python
•
GNU General Public License v3.0
•1•2•0•0•Updated Jul 30, 2026Jul 30, 2026
phenocal
Public
Genome-anchored calibration of a continuous phenotype across cohorts, with uncertainty-propagated probabilistic labels
rust machine-learning bioinformatics
rust machine-learning bioinformatics genomics weak-supervision uncertainty-quantification mic batch-effects cgmlst antimicrobial-resistance
Rust
•
MIT License
•0•0•0•0•Updated Jul 29, 2026Jul 29, 2026
mm2-geo
Public
Geometry-guided band-doubling for the minimap2 gap-filling DP (faster at identical variant-calling F1; composes with mm2-fast)
C
•
Other
•0•0•0•0•Updated Jul 25, 2026Jul 25, 2026
mm2-geo-reproducibility
Public
Reproducibility material (scripts, data manifests, seeds) for the mm2-geo paper
Shell
•
MIT License
•0•0•0•0•Updated Jul 24, 2026Jul 24, 2026
grapetree-rs
Public
Fast Rust port of GrapeTree's tree/distance engine (experimental)
rust bioinformatics phylogenetics
rust bioinformatics phylogenetics mlst neighbor-joining newick cgmlst minimum-spanning-tree genomic-surveillance mstree
Rust
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 23, 2026Jul 23, 2026
cgmlst-dists-rs
Public
Ultra-fast SIMD (AVX-512) pairwise cgMLST Hamming distance matrix — Rust reimplementation of cgmlst-dists-py, byte-identical output, ~6x faster than the C cgmls…
rust bioinformatics genomics
rust bioinformatics genomics simd mlst hamming-distance cgmlst genomic-surveillance chewbbaca
Rust
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 22, 2026Jul 22, 2026
freemap
Public
Trajectory-based long-read aligner with DP-free CIGAR generation
rust bioinformatics nanopore
rust bioinformatics nanopore genomics alignment pacbio sequence-alignment long-reads minimap2
Rust
•
MIT License
•0•0•0•0•Updated Jul 8, 2026Jul 8, 2026
wgs-nomenclature-proposal
Public
Draft proposal: interactive playground for an invariant, decentralised WGS nomenclature (LINcode-style; BTV/WNV)
HTML
•0•0•0•0•Updated Jul 1, 2026Jul 1, 2026
chewcall
Public
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 chewBBAC…
rust bioinformatics genomics
rust bioinformatics genomics smith-waterman mlst cgmlst wgmlst allele-calling parasail foodborne-pathogens
Rust
•0•3•0•0•Updated Jun 30, 2026Jun 30, 2026
cohesive-llm-benchmark
Public
End-to-end benchmark for natural-language to Nextflow pipeline generators targeting cohesive-ngsmanager.
Python
•0•0•0•0•Updated Jun 15, 2026Jun 15, 2026
spread
Public
Project based on GrapeTree, a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metad…
bioinformatics surveillance phylogenetics
bioinformatics surveillance phylogenetics
CSS
•
GNU General Public License v3.0
•0•12•0•0•Updated Jun 11, 2026Jun 11, 2026
wiki-engine
Public
A Docker-based documentation system combining MkDocs and Word document generation.
Python
•0•1•0•0•Updated May 27, 2026May 27, 2026
cgDist
Public
Ultra-fast SNP/indel-level distance calculator for core genome MLST analysis in bacterial genomics
rust bioinformatics genomics
rust bioinformatics genomics phylogenetics epidemiology mlst cgmlst snp-analysis food-safety outbreak-investigation
Rust
•
MIT License
•0•6•0•0•Updated May 27, 2026May 27, 2026
cohesive-llm
Public
Self-hostable AI platform that generates Nextflow DSL2 pipelines for the cohesive-ngsmanager framework
bioinformatics nextflow docker-compose
bioinformatics nextflow docker-compose ngs self-hosted caddy mistral rag fastapi authelia
Python
•
Other
•1•0•0•0•Updated Apr 27, 2026Apr 27, 2026
ohe-rs
Public
Ultra-fast one-hot encoding for bioinformatics and ML, powered by Rust + CUDA. Built for cgMLST allele profiles and large-scale categorical data.
python rust machine-learning
python rust machine-learning performance bioinformatics cuda pyo3 one-hot-encoding
Rust
•
MIT License
•0•1•0•0•Updated Apr 16, 2026Apr 16, 2026
dist2mst-rs
Public
Ultra-fast Minimum Spanning Tree construction from distance matrices — Rust rewrite of dist2mst (~900x faster)
rust bioinformatics genomics
rust bioinformatics genomics clustering high-performance phylogenetics newick minimum-spanning-tree distance-matrix
Rust
•
MIT License
•0•1•0•0•Updated Apr 15, 2026Apr 15, 2026
dist2mst
Public
High-performance Minimum Spanning Tree construction from distance matrices with Numba acceleration
bioinformatics genomics clustering
bioinformatics genomics clustering phylogenetics numba newick minimum-spanning-trees minimum-spanning-tree distance-matrix
Python
•
MIT License
•0•2•0•0•Updated Apr 15, 2026Apr 15, 2026
chewBBACA
Public
BSR-Based Allele Calling Algorithm
HTML
•
GNU General Public License v3.0
•34•0•0•0•Updated Mar 11, 2026Mar 11, 2026
cohesive-cmdbuild-builder
Public
Shell
•0•0•0•0•Updated Mar 2, 2026Mar 2, 2026
coreguard
Public
CoreGuard - SNP comparison visualization tool for multi-pipeline genomic analysis. Compare SNP calls from different variant calling pipelines (Snippy, CFSAN, et…
visualization rust bioinformatics
visualization rust bioinformatics genomics nextflow webassembly snp variant-calling
Rust
•
MIT License
•0•1•0•0•Updated Feb 8, 2026Feb 8, 2026
cohesive-ngsmanager-cli
Public
Shell
•0•0•0•0•Updated Feb 4, 2026Feb 4, 2026
GenomicBasedRegression
Public
Script performing regression-based training or prediction from categorical genomic data
Python
•
GNU General Public License v3.0
•2•0•0•0•Updated Dec 17, 2025Dec 17, 2025
GenomicBasedClassification
Public
Script performing classification-based modeling or prediction from genomic data
Python
•
GNU General Public License v3.0
•2•0•0•0•Updated Dec 17, 2025Dec 17, 2025
cohesive
Public
Docker-based COHESIVE Information System (CIS) for One Health surveillance, outbreak investigation, and risk assessment of zoonoses.
bioinformatics public-health clustering-analysis
bioinformatics public-health clustering-analysis outbreaks one-health outbreak-investigation foodborne-diseases diseases-surveillance
Groovy
•
GNU Affero General Public License v3.0
•0•1•0•0•Updated Oct 14, 2025Oct 14, 2025
cohesive-auspice
Public
JavaScript
•
GNU Affero General Public License v3.0
•0•0•0•0•Updated Oct 13, 2025Oct 13, 2025
cohesive-cmdbuild
Public
JavaScript
•
Other
•0•0•0•0•Updated Oct 13, 2025Oct 13, 2025
cohesive-bioinfotoolsweb2
Public
Java
•
MIT License
•0•0•0•0•Updated Oct 13, 2025Oct 13, 2025
cohesive-zuul
Public
Java
•
MIT License
•0•0•0•0•Updated Oct 13, 2025Oct 13, 2025
cohesive-bioinfotools2
Public
Java
•
MIT License
•0•0•0•0•Updated Oct 13, 2025Oct 13, 2025
cohesive-common-resources
Public
JavaScript
•
MIT License
•0•0•0•0•Updated Oct 13, 2025Oct 13, 2025

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

All

All

49 repositories

cgmlst-dists-py

phenocal

mm2-geo

mm2-geo-reproducibility

grapetree-rs

cgmlst-dists-rs

freemap

wgs-nomenclature-proposal

chewcall

cohesive-llm-benchmark

spread

wiki-engine

cgDist

cohesive-llm

ohe-rs

dist2mst-rs

dist2mst

chewBBACA

cohesive-cmdbuild-builder

coreguard

cohesive-ngsmanager-cli

GenomicBasedRegression

GenomicBasedClassification

cohesive

cohesive-auspice

cohesive-cmdbuild

cohesive-bioinfotoolsweb2

cohesive-zuul

cohesive-bioinfotools2

cohesive-common-resources

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Repositories list

49 repositories