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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 7 1

  2. 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 6 1

  3. VIPERA VIPERA Public

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

    Python 4

  4. mycolorsTB mycolorsTB Public

    R Color package for Mycobacterium tuberculosis complex

    R 4

  5. transcluster transcluster Public

    A Snakemake workflow to find SARS-CoV-2 clusters in a reference phylogeny and estimate their transmission fitness

    Python 2

  6. misb_training_2024 misb_training_2024 Public

    Master on Integrative Synthetic Biology (MISB) training sessions 2024

    Jupyter Notebook 1

Repositories

Showing 10 of 11 repositories
  • 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 Jan 30, 2025
  • transcluster Public

    A Snakemake workflow to find SARS-CoV-2 clusters in a reference phylogeny and estimate their transmission fitness

    PathoGenOmics-Lab/transcluster’s past year of commit activity
    Python 2 GPL-3.0 0 0 0 Updated Jan 29, 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 6 GPL-3.0 1 0 0 Updated Dec 4, 2024
  • 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 7 GPL-3.0 1 0 0 Updated Nov 20, 2024
  • SARStools Public
    PathoGenOmics-Lab/SARStools’s past year of commit activity
    Python 0 0 0 0 Updated Jul 4, 2024
  • CrossInfectMTB Public

    Repo for bioinformatic analysis about MTB infections

    PathoGenOmics-Lab/CrossInfectMTB’s past year of commit activity
    Shell 0 GPL-3.0 0 0 0 Updated Jun 19, 2024
  • 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 Jun 17, 2024
  • misb_training_2024 Public

    Master on Integrative Synthetic Biology (MISB) training sessions 2024

    PathoGenOmics-Lab/misb_training_2024’s past year of commit activity
    Jupyter Notebook 1 GPL-3.0 0 0 0 Updated May 15, 2024
  • 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 4 GPL-3.0 0 0 0 Updated Apr 17, 2024
  • mycolorsTB Public

    R Color package for Mycobacterium tuberculosis complex

    PathoGenOmics-Lab/mycolorsTB’s past year of commit activity
    R 4 GPL-3.0 0 0 0 Updated Apr 4, 2024
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