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@genpat-it

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

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  1. spread spread Public

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

    CSS 12

  2. cgDist cgDist Public

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

    Rust 7

  3. chewcall 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 chewBBACA with 100% DNA-sequence agreement on…

    Rust 3

  4. cgmlst-dists-py cgmlst-dists-py Public

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

    Python 2 1

  5. dist2mst dist2mst Public

    High-performance Minimum Spanning Tree construction from distance matrices with Numba acceleration

    Python 2

  6. cohesive cohesive Public

    Docker-based COHESIVE Information System (CIS) for One Health surveillance, outbreak investigation, and risk assessment of zoonoses.

    Groovy 1

Repositories

Showing 10 of 49 repositories
  • cgDist Public

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

    genpat-it/cgDist's past year of commit activity
    Rust 7 MIT 0 0 0 Updated Sep 4, 2026
  • spread Public

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

    genpat-it/spread's past year of commit activity
    CSS 12 GPL-3.0 0 0 0 Updated Sep 1, 2026
  • cohesive-llm Public

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

    genpat-it/cohesive-llm's past year of commit activity
    Python 0 1 0 0 Updated Aug 31, 2026
  • cgmlst-dists-py Public

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

    genpat-it/cgmlst-dists-py's past year of commit activity
    Python 2 GPL-3.0 1 0 0 Updated Jul 30, 2026
  • phenocal Public

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

    genpat-it/phenocal's past year of commit activity
    Rust 0 MIT 0 0 0 Updated Jul 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)

    genpat-it/mm2-geo's past year of commit activity
    C 0 0 0 0 Updated Jul 25, 2026
  • mm2-geo-reproducibility Public

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

    genpat-it/mm2-geo-reproducibility's past year of commit activity
    Shell 0 MIT 0 0 0 Updated Jul 24, 2026
  • grapetree-rs Public

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

    genpat-it/grapetree-rs's past year of commit activity
    Rust 0 GPL-3.0 0 0 0 Updated Jul 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 cgmlst-dists

    genpat-it/cgmlst-dists-rs's past year of commit activity
    Rust 0 GPL-3.0 0 0 0 Updated Jul 22, 2026
  • freemap Public

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

    genpat-it/freemap's past year of commit activity
    Rust 0 MIT 0 0 0 Updated Jul 8, 2026
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