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    53 repositories

    • pango-watch

      Public
      HTML
      •3•1•2•0•Updated Aug 21, 2025Aug 21, 2025

    • github-watch

      Public
      Python
      •1•0•2•0•Updated Aug 14, 2025Aug 14, 2025

    • bohra

      Public
      A pipeline for bioinformatics analysis of bacterial genomes
      nextflowbioinformatics-pipelinemicrobial-genomicsmdu-phlbioinformatics
      Nextflow
      •
      GNU General Public License v3.0
      •5•31•10•0•Updated Aug 13, 2025Aug 13, 2025

    • himal_scripts

      Public
      Some scripts for MDU data
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 6, 2025Aug 6, 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

    • mlstdb

      Public
      A Python package to update the MLST database for the mlst tool.
      Python
      •
      MIT License
      •0•3•2•0•Updated Jul 16, 2025Jul 16, 2025

    • tbtamr

      Public
      AMR inference for Mtb - cousin to abriTAMR
      Python
      •
      GNU General Public License v3.0
      •4•5•1•0•Updated Jun 11, 2025Jun 11, 2025

    • ngmaster

      Public
      In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
      Python
      •
      GNU General Public License v3.0
      •5•8•10•2•Updated Apr 28, 2025Apr 28, 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-annotationgenotypingstreptococcus-pyogenesemm-typing
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •6•12•15•0•Updated Mar 25, 2025Mar 25, 2025

    • meningotype

      Public
      In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis
      Python
      •
      GNU General Public License v3.0
      •9•15•12•2•Updated Feb 2, 2025Feb 2, 2025

    • hicap

      Public
      👋🎓 in silico typing of the H. influenzae cap locus
      Python
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Feb 1, 2025Feb 1, 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 Oct 3, 2024Oct 3, 2024

    • abritamr

      Public
      A pipeline for running AMRfinderPlus and collating results into functional classes
      Python
      •17•81•10•2•Updated Aug 19, 2024Aug 19, 2024

    • pango-collapse

      Public
      app to collapse Pango lineages for reporting
      Python
      •
      GNU General Public License v3.0
      •2•13•3•0•Updated Mar 20, 2024Mar 20, 2024

    • Raquel_test

      Public
      Testing :-)
      0•0•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
      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

    • LisSero

      Public
      In silico serotype prediction for Listeria monocytogenes
      bioinformaticspublic-healthmicrobial-genomicsserotypinglisteria-monocytogenes
      Python
      •
      GNU General Public License v3.0
      •9•7•6•6•Updated Feb 26, 2023Feb 26, 2023

    • covid-venn

      Public
      Shiny app for creating Venn diagrams of SARS-CoV-2 variant/lineage mutations.
      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
      •42•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
      •10•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

    • who2tbp

      Public
      A script to convert WHO MTB resistant variants to a format that can be ingested by TBProfiler
      Python
      •2•1•1•0•Updated Jan 28, 2022Jan 28, 2022

    • COVID19-paper

      Public
      Data for publications related to Victorian SARS-CoV-2 genomic epidemiology
      genomicsaustraliacovid19-datapublic-health-microbiology
      GNU General Public License v3.0
      •1•1•2•0•Updated Nov 12, 2021Nov 12, 2021

    • CPE-Paper

      Public
      Data for publications related to Victorian CPE surveillance and genomic epidemiology
      0•0•0•0•Updated Jul 30, 2021Jul 30, 2021

    • arbow

      Public archive
      Cultivate your multiple sequence alignments to get better trees
      bioinformaticsphylogenetic-treesmultiple-sequence-alignment
      Python
      •1•6•5•1•Updated Apr 20, 2021Apr 20, 2021