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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 9 2

  2. VIPERA VIPERA Public

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

    Python 8 1

  3. 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 7 1

  4. fstic fstic Public

    Calculates pairwise distances between samples using alelle frequencies

    Rust 6

  5. mycolorsTB mycolorsTB Public

    R Color package for Mycobacterium tuberculosis complex

    R 5

  6. distree distree Public

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

    Rust 3

Repositories

Showing 10 of 14 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 1 0 1 Updated Jan 2, 2026
  • fstic Public

    Calculates pairwise distances between samples using alelle frequencies

    PathoGenOmics-Lab/fstic’s past year of commit activity
    Rust 6 GPL-3.0 0 0 0 Updated Aug 12, 2025
  • 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 Aug 12, 2025
  • 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
  • ena-spike-ntd-repdel-analysis Public

    A Snakemake workflow with associated scripts used for detecting spike NTD repaired deletions in SARS-CoV-2 Omicron BA.1 lineage reads. Manuscript under review.

    PathoGenOmics-Lab/ena-spike-ntd-repdel-analysis’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated May 2, 2025
  • 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 7 GPL-3.0 1 0 0 Updated Feb 21, 2025
  • 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 9 GPL-3.0 2 0 0 Updated Nov 20, 2024
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