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42 repositories

chewcall
Public
Fast allele caller for cgMLST/wgMLST schemas, compatible with chewBBACA. 6-10x faster with SIMD Smith-Waterman (parasail).
rust bioinformatics genomics
rust bioinformatics genomics smith-waterman mlst cgmlst wgmlst allele-calling parasail foodborne-pathogens
Rust
•0•0•0•0•Updated Apr 22, 2026Apr 22, 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•0•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•0•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
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•1•1•0•Updated Apr 14, 2026Apr 14, 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 10, 2026Apr 10, 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 Mar 17, 2026Mar 17, 2026
chewBBACA
Public
BSR-Based Allele Calling Algorithm
HTML
•
GNU General Public License v3.0
•32•0•0•0•Updated Mar 11, 2026Mar 11, 2026
wiki-engine
Public
A Docker-based documentation system combining MkDocs and Word document generation.
Python
•0•1•0•0•Updated Mar 7, 2026Mar 7, 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•0•0•0•Updated Feb 8, 2026Feb 8, 2026
cohesive-ngsmanager-cli
Public
Shell
•0•0•0•0•Updated Feb 4, 2026Feb 4, 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 recombination-detection
Rust
•
MIT License
•0•3•0•0•Updated Dec 22, 2025Dec 22, 2025
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
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•10•0•0•Updated Oct 16, 2025Oct 16, 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
cohesive-auspice-server
Public
Java
•
MIT License
•0•0•0•0•Updated Oct 13, 2025Oct 13, 2025
campy-ml
Public
Python
•0•0•0•0•Updated Sep 22, 2025Sep 22, 2025
cgDist-surveillance
Public
Shell
•0•0•0•0•Updated Aug 28, 2025Aug 28, 2025
cohesive-ngsmanager
Public
Nextflow
•
GNU Affero General Public License v3.0
•3•0•0•0•Updated May 15, 2025May 15, 2025
mkdocs-packages
Public
Collection of MkDocs packages we use to build our documentation
JavaScript
•0•0•0•0•Updated Feb 11, 2025Feb 11, 2025
jstree
Public
jquery tree plugin (for searching time improvement)
JavaScript
•
MIT License
•1.4k•0•0•0•Updated Sep 3, 2024Sep 3, 2024
cohesive-jenkins
Public
GNU Affero General Public License v3.0
•1•0•0•0•Updated May 31, 2024May 31, 2024

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

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All

42 repositories

chewcall

ohe-rs

dist2mst-rs

dist2mst

cgmlst-dists-py

cohesive-llm

freemap

chewBBACA

wiki-engine

cohesive-cmdbuild-builder

coreguard

cohesive-ngsmanager-cli

cgDist

GenomicBasedRegression

GenomicBasedClassification

spread

cohesive

cohesive-auspice

cohesive-cmdbuild

cohesive-bioinfotoolsweb2

cohesive-zuul

cohesive-bioinfotools2

cohesive-common-resources

cohesive-auspice-server

campy-ml

cgDist-surveillance

cohesive-ngsmanager

mkdocs-packages

jstree

cohesive-jenkins

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All

Repositories list

42 repositories