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@PathoGenOmics-Lab

PathoGenOmics Lab

An interdisciplinary research group dedicated to unraveling the complexities of microbial pathogens and their relationships with hosts.

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  1. snpick snpick Public

    snpick is a fast and memory-efficient Rust-based SNP extraction tool designed to handle large genomic alignments with minimal RAM usage and high-speed performance.

    Rust 12 2

  2. pathotypr pathotypr Public

    Genome classificator using machine learning and SNP markers.

    JavaScript 10

  3. VIPERA VIPERA Public

    A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis

    Python 8

  4. get_MNV get_MNV Public

    Identifies multiple SNVs within the same codon, reclassifies them as MNVs, and accurately computes resulting amino acid changes from genomic reads

    Rust 8 1

  5. fstic fstic Public

    Calculates pairwise distances between samples using alelle frequencies

    Rust 7

  6. mycolorsTB mycolorsTB Public

    R Color package for Mycobacterium tuberculosis complex

    R 5

Repositories

Showing 10 of 15 repositories
  • VIPERA Public

    A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis

    PathoGenOmics-Lab/VIPERA’s past year of commit activity
    Python 8 GPL-3.0 0 0 2 Updated Apr 17, 2026
  • get_MNV Public

    Identifies multiple SNVs within the same codon, reclassifies them as MNVs, and accurately computes resulting amino acid changes from genomic reads

    PathoGenOmics-Lab/get_MNV’s past year of commit activity
    Rust 8 AGPL-3.0 1 0 0 Updated Apr 14, 2026
  • distree Public

    Extracts a distance matrix from a phylogeny (parallel, low-memory)

    PathoGenOmics-Lab/distree’s past year of commit activity
    Rust 3 GPL-3.0 0 0 0 Updated Apr 4, 2026
  • fstic Public

    Calculates pairwise distances between samples using alelle frequencies

    PathoGenOmics-Lab/fstic’s past year of commit activity
    Rust 7 GPL-3.0 0 0 0 Updated Apr 4, 2026
  • snpick Public

    snpick is a fast and memory-efficient Rust-based SNP extraction tool designed to handle large genomic alignments with minimal RAM usage and high-speed performance.

    PathoGenOmics-Lab/snpick’s past year of commit activity
    Rust 12 GPL-3.0 2 0 0 Updated Mar 31, 2026
  • pathotypr Public

    Genome classificator using machine learning and SNP markers.

    PathoGenOmics-Lab/pathotypr’s past year of commit activity
    JavaScript 10 AGPL-3.0 0 0 0 Updated Mar 29, 2026
  • afwdist Public

    A lightweight tool to calculate a pairwise distance metric based on fixed and non-fixed allele frequencies

    PathoGenOmics-Lab/afwdist’s past year of commit activity
    Rust 0 GPL-3.0 0 0 0 Updated Aug 6, 2025
  • mycolorsTB Public

    R Color package for Mycobacterium tuberculosis complex

    PathoGenOmics-Lab/mycolorsTB’s past year of commit activity
    R 5 GPL-3.0 0 0 0 Updated Aug 1, 2025
  • transcluster Public

    A Snakemake workflow to find SARS-CoV-2 clusters in a reference phylogeny and estimate their normalized clustering index

    PathoGenOmics-Lab/transcluster’s past year of commit activity
    Python 2 GPL-3.0 0 0 0 Updated May 2, 2025
  • tcfinder Public

    A lightweight tool to find clusters of samples within a phylogeny

    PathoGenOmics-Lab/tcfinder’s past year of commit activity
    Rust 1 GPL-3.0 0 0 0 Updated May 2, 2025
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