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@MDU-PHL Microbiological Diagnostic Unit Public Health Laboratory

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    57 repositories

    • himal_scripts

      Public
      Some scripts for MDU data
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 4, 2026Sep 4, 2026

    • abritamr

      Public
      A pipeline for running AMRfinderPlus and collating results into functional classes
      Python
      •
      GNU General Public License v3.0
      •18•102•27•0•Updated Aug 30, 2026Aug 30, 2026

    • github-watch

      Public
      Python
      •1•0•2•0•Updated Aug 19, 2026Aug 19, 2026

    • mlstdb

      Public
      A Python package to update the MLST database for the mlst tool.
      Python
      •
      GNU General Public License v3.0
      •1•32•8•0•Updated Jul 22, 2026Jul 22, 2026

    • bohra

      Public
      A pipeline for bioinformatics analysis of bacterial genomes
      bioinformaticsnextflowbioinformatics-pipeline
      bioinformaticsnextflowbioinformatics-pipelinemicrobial-genomics
      Nextflow
      •
      GNU General Public License v3.0
      •5•34•16•2•Updated Jul 17, 2026Jul 17, 2026

    • ngmaster

      Public
      In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
      Python
      •
      GNU General Public License v3.0
      •4•10•1•0•Updated Jun 17, 2026Jun 17, 2026

    • cgmlst-dists

      Public
      🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
      C
      •
      GNU General Public License v3.0
      •8•0•0•0•Updated Jun 12, 2026Jun 12, 2026

    • tbtamr

      Public
      AMR inference for Mtb - cousin to abriTAMR
      Python
      •
      GNU General Public License v3.0
      •4•7•5•0•Updated May 11, 2026May 11, 2026

    • pango-watch

      Public
      HTML
      •3•1•3•0•Updated Mar 16, 2026Mar 16, 2026

    • LisSero

      Public
      In silico serotype prediction for Listeria monocytogenes
      bioinformaticspublic-healthmicrobial-genomics
      bioinformaticspublic-healthmicrobial-genomicsserotypinglisteria-monocytogenes
      Python
      •
      GNU General Public License v3.0
      •10•11•7•6•Updated Feb 23, 2026Feb 23, 2026

    • meningotype

      Public
      In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis
      Python
      •
      GNU General Public License v3.0
      •10•16•18•4•Updated Feb 19, 2026Feb 19, 2026

    • pango-collapse

      Public
      app to collapse Pango lineages for reporting
      Python
      •
      GNU General Public License v3.0
      •1•13•2•1•Updated Dec 9, 2025Dec 9, 2025

    • bohra-mdu

      Public
      A pipeline for bioinformatics analysis of bacterial genomes
      Nextflow
      •
      GNU General Public License v3.0
      •5•0•5•0•Updated Nov 6, 2025Nov 6, 2025

    • covdrop

      Public
      Python
      •1•0•1•0•Updated Nov 1, 2025Nov 1, 2025

    • abritamr-mdu

      Public
      A pipeline for running AMRfinderPlus and collating results into functional classes
      Python
      •18•0•0•0•Updated Oct 14, 2025Oct 14, 2025

    • mutamr

      Public
      stripped down tool for generation of annotated vcf from paired-end reads
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • QRate

      Public
      This repo contains scripts to process `standard_bacteria_qc.csv` file obtained from the `mdudatagen` pipeline.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • salmonella_typing

      Public
      Salmonella serotyping at MDU
      Python
      •0•1•14•1•Updated Apr 1, 2025Apr 1, 2025

    • emmtyper

      Public
      emm Automatic Isolate Labeller
      bioinformaticsgenome-annotationgenotyping
      bioinformaticsgenome-annotationgenotypingstreptococcus-pyogenesemm-typing
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •5•15•17•1•Updated Mar 25, 2025Mar 25, 2025

    • hicap

      Public
      👋🎓 in silico typing of the H. influenzae cap locus
      Python
      •
      GNU General Public License v3.0
      •6•0•0•0•Updated Feb 1, 2025Feb 1, 2025

    • Raquel_test

      Public
      Testing :-)
      0•1•0•0•Updated Oct 26, 2023Oct 26, 2023

    • kristy_helper_scripts

      Public
      Some helpful (or not) scripts for wrangling MDU data
      Python
      •0•0•0•0•Updated Oct 26, 2023Oct 26, 2023

    • babykraken

      Public
      0•2•0•0•Updated Apr 4, 2023Apr 4, 2023

    • dcompressee

      Public
      A small library to return temporary decompressed files when one needs them.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 22, 2023Mar 22, 2023

    • vezzo

      Public
      A small library to verify that compatible versions of dependencies are installed before your tool can run properly.
      librarybioinformaticsdependencies
      librarybioinformaticsdependencies
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 17, 2023Mar 17, 2023

    • rezzie

      Public
      A small library for accessing resources and data shipped with your package without using the pkg_resources API.
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 17, 2023Mar 17, 2023

    • covid-venn

      Public
      Shiny app for creating Venn diagrams of SARS-CoV-2 variant/lineage mutations.
      covidsars-cov-2sars-cov-2-variants
      covidsars-cov-2sars-cov-2-variants
      R
      •
      MIT License
      •0•0•1•0•Updated Dec 8, 2022Dec 8, 2022

    • TBProfiler

      Public
      Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
      Python
      •
      GNU General Public License v3.0
      •46•0•0•0•Updated Jun 16, 2022Jun 16, 2022

    • pathogen-profiler

      Public
      This repository contains python classes and functions to quickly create a profiling tool for pathogen NGS data
      Python
      •
      GNU Lesser General Public License v3.0
      •11•0•0•0•Updated Jun 9, 2022Jun 9, 2022

    • cleptr

      Public
      A nomenclature generator for cgMLST reporting
      Python
      •0•0•0•0•Updated May 25, 2022May 25, 2022
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