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

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39 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 Mar 19, 2026Mar 19, 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
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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
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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
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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
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GNU Affero General Public License v3.0
•0•1•0•0•Updated Oct 14, 2025Oct 14, 2025
cohesive-auspice
Public
JavaScript
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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
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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
dist2mst
Public
High-performance tool for constructing Minimum Spanning Trees from symmetric distance matrices. Features Numba-accelerated algorithms, parallel processing, and …
bioinformatics newick minimum-spanning-trees
bioinformatics newick minimum-spanning-trees distance-matrix
Python
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MIT License
•0•2•0•0•Updated Jul 27, 2025Jul 27, 2025
cohesive-ngsmanager
Public
Nextflow
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GNU Affero General Public License v3.0
•3•0•0•0•Updated May 15, 2025May 15, 2025
cgmlst-dists-py
Public
The python multithreaded version of the famous cgmlst-dists bioinformatic tool by Torsten Seemann
bioinformatics distance-calculation cgmlst
bioinformatics distance-calculation cgmlst bioinformatics-tool cgmlst-genes
Python
•0•1•0•0•Updated Mar 17, 2025Mar 17, 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
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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
cohesive-images
Public
0•0•0•0•Updated May 31, 2024May 31, 2024
wiki-engine-old
Public archive
Dockerfile
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GNU General Public License v3.0
•0•0•0•0•Updated May 31, 2024May 31, 2024
MSTreesV2_POC
Public
GrapeTree for large datasets
bioinformatics phylogenetics phylogenomics
bioinformatics phylogenetics phylogenomics
Python
•0•0•0•0•Updated May 22, 2024May 22, 2024