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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 13

  2. cgDist cgDist Public

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

    Rust 9 2

  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. cohesive cohesive Public

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

    Groovy 2

  6. dist2mst dist2mst Public

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

    Python 2

Repositories

Showing 10 of 50 repositories
  • 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 1 0 0 0 Updated Oct 22, 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 chewBBACA with 100% DNA-sequence agreement on bilaterally callable cells.

    genpat-it/chewcall's past year of commit activity
    Rust 3 GPL-3.0 0 0 0 Updated Oct 17, 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 Oct 13, 2026
  • mm2-geo-reproducibility Public

    Superseded: first-submission material of mm2-geo; current version on branch 'reproducibility' of genpat-it/mm2-geo

    genpat-it/mm2-geo-reproducibility's past year of commit activity
    Shell 0 MIT 0 0 0 Updated Oct 12, 2026
  • 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 9 MIT 2 0 0 Updated Oct 2, 2026
  • bioinformatics-platform-comparison Public

    Documented, correctable comparison of bacterial and viral genomic-surveillance platforms: every value backed by a cited source and a verbatim passage. Corrections via pull request.

    genpat-it/bioinformatics-platform-comparison's past year of commit activity
    HTML 1 0 0 0 Updated Oct 2, 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 1 1 0 0 Updated Sep 25, 2026
  • cohesive-jenkins Public
    genpat-it/cohesive-jenkins's past year of commit activity
    1 AGPL-3.0 1 0 1 Updated Sep 19, 2026
  • cohesive-ngsmanager Public
    genpat-it/cohesive-ngsmanager's past year of commit activity
    Nextflow 0 AGPL-3.0 3 0 0 Updated Sep 19, 2026
  • cohesive Public

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

    genpat-it/cohesive's past year of commit activity
    Groovy 2 AGPL-3.0 0 0 0 Updated Sep 19, 2026
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