Repositories list

• ngmaster

  Public
  In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)

  Python

  •

  GNU General Public License v3.0

  •4•9•12•3•Updated Mar 26, 2026Mar 26, 2026

• bohra

  Public
  A pipeline for bioinformatics analysis of bacterial genomes

  bioinformaticsnextflowbioinformatics-pipeline+ 1

  bioinformaticsnextflowbioinformatics-pipelinemicrobial-genomics

  Nextflow

  •

  GNU General Public License v3.0

  •5•32•21•0•Updated Mar 25, 2026Mar 25, 2026

• mlstdb

  Public
  A Python package to update the MLST database for the mlst tool.

  Python

  •

  GNU General Public License v3.0

  •1•19•7•0•Updated Mar 24, 2026Mar 24, 2026

• abritamr

  Public
  A pipeline for running AMRfinderPlus and collating results into functional classes

  Python

  •

  GNU General Public License v3.0

  •18•92•20•0•Updated Mar 21, 2026Mar 21, 2026

• github-watch

  Public
  Python

  •1•0•2•0•Updated Mar 17, 2026Mar 17, 2026

• pango-watch

  Public
  HTML

  •3•1•2•0•Updated Mar 16, 2026Mar 16, 2026

• himal_scripts

  Public
  Some scripts for MDU data

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Feb 26, 2026Feb 26, 2026

• LisSero

  Public
  In silico serotype prediction for Listeria monocytogenes

  bioinformaticspublic-healthmicrobial-genomics+ 2

  bioinformaticspublic-healthmicrobial-genomicsserotypinglisteria-monocytogenes

  Python

  •

  GNU General Public License v3.0

  •10•9•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

  •9•15•16•3•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•0•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•3•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

• tbtamr

  Public
  AMR inference for Mtb - cousin to abriTAMR

  Python

  •

  GNU General Public License v3.0

  •4•7•3•0•Updated Jun 11, 2025Jun 11, 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+ 2

  bioinformaticsgenome-annotationgenotypingstreptococcus-pyogenesemm-typing

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •5•12•16•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

  •4•0•0•0•Updated Feb 1, 2025Feb 1, 2025

• 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

  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

  •45•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

• who2tbp

  Public
  A script to convert WHO MTB resistant variants to a format that can be ingested by TBProfiler

  Python

  •2•2•1•0•Updated Jan 28, 2022Jan 28, 2022