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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 17 2

  2. pathotypr pathotypr Public

    Genome classificator using machine learning and SNP markers

    JavaScript 13 1

  3. get_MNV get_MNV Public

    Turns same-codon SNVs into MNVs and computes the true amino acid change

    Rust 11 2

  4. fstic fstic Public

    Calculates pairwise distances between samples using alelle frequencies

    Rust 9

  5. VIPERA VIPERA Public

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

    Python 8

  6. mycolorsTB mycolorsTB Public

    R Color package for Mycobacterium tuberculosis complex

    R 7

Repositories

Showing 10 of 18 repositories
  • karyon Public

    Genomic track plots for Rust: composable tracks over a shared coordinate axis, rendered to standalone SVG with zero dependencies

    PathoGenOmics-Lab/karyon's past year of commit activity
    Rust 3 MIT 0 0 5 Updated Oct 31, 2026
  • pathotypr Public

    Genome classificator using machine learning and SNP markers

    PathoGenOmics-Lab/pathotypr's past year of commit activity
    JavaScript 13 AGPL-3.0 1 0 1 Updated Oct 31, 2026
  • get_MNV Public

    Turns same-codon SNVs into MNVs and computes the true amino acid change

    PathoGenOmics-Lab/get_MNV's past year of commit activity
    Rust 11 AGPL-3.0 2 0 1 Updated Oct 31, 2026
  • recore Public

    Post-hoc rescue and quality control of pangenome presence/absence matrices

    PathoGenOmics-Lab/recore's past year of commit activity
    Rust 0 AGPL-3.0 0 0 0 Updated Oct 30, 2026
  • AMAP Public

    🍃Automated (re)annotation pipeline for MTBC genomes

    PathoGenOmics-Lab/AMAP's past year of commit activity
    Python 1 GPL-3.0 0 0 0 Updated Oct 25, 2026
  • eskaks Public

    Calculates dN/dS for sequences

    PathoGenOmics-Lab/eskaks's past year of commit activity
    Rust 4 GPL-3.0 0 0 0 Updated Oct 19, 2026
  • fstic Public

    Calculates pairwise distances between samples using alelle frequencies

    PathoGenOmics-Lab/fstic's past year of commit activity
    Rust 9 GPL-3.0 0 0 0 Updated Oct 1, 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 17 GPL-3.0 2 0 0 Updated Oct 1, 2026
  • distree Public

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

    PathoGenOmics-Lab/distree's past year of commit activity
    Rust 5 GPL-3.0 0 0 0 Updated Oct 1, 2026
  • BAMpiro Public

    General Bacterial Short Read Mapping, Variant Calling & Lineage/DR Typing Pipeline

    PathoGenOmics-Lab/BAMpiro's past year of commit activity
    Python 1 GPL-3.0 0 0 0 Updated Sep 24, 2026
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