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@genpat-it GENPAT (Italian National Reference Centre for WGS of microbial pathogens)

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    21 repositories

    • wiki-engine

      Public
      A Docker-based documentation system combining MkDocs and Word document generation.
      Python
      •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

    • dist2mst

      Public
      High-performance tool for constructing Minimum Spanning Trees from symmetric distance matrices. Features Numba-accelerated algorithms, parallel processing, and zero-distance grouping. Outputs MST in standard Newick format.
      bioinformaticsnewickminimum-spanning-treesdistance-matrix
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

    • spread

      Public
      Project based on GrapeTree, a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata.
      bioinformaticssurveillancephylogenetics
      CSS
      •
      GNU General Public License v3.0
      •0•6•0•0•Updated Feb 19, 2025Feb 19, 2025

    • cgmlst-dists-py

      Public
      The python multithreaded version of the famous cgmlst-dists bioinformatic tool by Torsten Seemann
      bioinformaticsdistance-calculationcgmlstbioinformatics-toolcgmlst-genes
      Python
      •0•0•0•0•Updated Feb 13, 2025Feb 13, 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

    • cgdist

      Public
      0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

    • cohesive-ngsmanager

      Public
      Nextflow
      •
      GNU Affero General Public License v3.0
      •1•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • cohesive

      Public
      Groovy
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 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
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 31, 2024May 31, 2024

    • MSTreesV2_POC

      Public
      GrapeTree for large datasets
      bioinformaticsphylogeneticsphylogenomics
      Python
      •0•0•0•0•Updated May 22, 2024May 22, 2024

    • vcf2mst

      Public
      Hamming Distance based Minimum Spanning Tree from Samples vcf using graptree
      Perl
      •
      GNU General Public License v3.0
      •3•0•1•0•Updated May 15, 2024May 15, 2024

    • ngsmanager

      Public
      Bioinformatic pipeline of the GENPAT platform
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 23, 2023Nov 23, 2023

    • grapetree-gis

      Public
      Project based on GrapeTree, a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata.
      JavaScript
      •0•0•0•0•Updated Oct 10, 2023Oct 10, 2023

    • cgmlst-dists

      Public
      🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
      C
      •
      GNU General Public License v3.0
      •7•0•0•0•Updated Sep 26, 2023Sep 26, 2023

    • cgmlst-dists-64

      Public
      A fork of the cgmlst-dists program that has been modified to manage large files and uses 64-bit integers to calculate the size of distance vector.
      0•0•0•0•Updated Sep 26, 2023Sep 26, 2023

    • CIS

      Public
      0•0•0•0•Updated Oct 18, 2022Oct 18, 2022

    • PairwiseDifferencesToROC

      Public
      Script performing Receiver Operating Characteristic (ROC) analysis to identify thresholds of mutation pairwise differences from microbial genomes involved in an investigated outbreak
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 6, 2022Jan 6, 2022

    • TreeToCongruency

      Public
      Script comparing two trees through a tanglegram and estimations of congruency metrics
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 19, 2021Oct 19, 2021

    • genpat-dashboard

      Public
      GenPat-Dashboard web application
      JavaScript
      •1•0•0•0•Updated Jan 8, 2021Jan 8, 2021