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    16 repositories

    • C.jejuni-multilevel-HierCC-typing-scheme

      Public
      A workflow for accurate genotyping and surveillance of C.jejuni WGS genomes
      0•0•0•0•Updated Jan 12, 2026Jan 12, 2026

    • Scripts-MGT-S-aureus

      Public
      Additional scripts supplementing the development of MGT for Staphylococcus aureus.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 23, 2025Jun 23, 2025

    • dodge

      Public
      Dynamic Outbreak Detection for Genomic Epidemiology
      Python
      •
      GNU General Public License v3.0
      •2•4•0•0•Updated Sep 9, 2024Sep 9, 2024

    • MGT-local

      Public
      Install a local blank version of the MGT database
      JavaScript
      •
      GNU General Public License v3.0
      •2•2•1•0•Updated Jun 6, 2024Jun 6, 2024

    • debug-mpcr

      Public
      A script to examine amplicon sequencing of multiplex PCR assays
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 6, 2024Jun 6, 2024

    • salty

      Public
      The Staphylococcus aureus Lineage Typer (SaLTy)
      Python
      •
      GNU General Public License v3.0
      •0•7•0•0•Updated May 15, 2024May 15, 2024

    • STECFinder

      Public
      Clustering and Serotyping of Shigatoxin producing E. coli (STEC) using genomic cluster specific markers
      bioinformaticsgenomicsmicrobial-genomics
      bioinformaticsgenomicsmicrobial-genomics
      Python
      •
      GNU General Public License v3.0
      •3•5•0•0•Updated Mar 19, 2024Mar 19, 2024

    • campygstyper

      Public
      A python script for accurate assignment of ANI genomic species to Campylobacter genomes.
      Python
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Mar 14, 2024Mar 14, 2024

    • NestedProkkaFix

      Public
      Script to check for falsely split orthologues in roary outputs
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 1, 2023Nov 1, 2023

    • ShigEiFinder

      Public
      Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
      bioinformaticsgenomicsmicrobial-genomics
      bioinformaticsgenomicsmicrobial-genomics
      Python
      •
      GNU General Public License v3.0
      •2•13•0•0•Updated Jun 30, 2023Jun 30, 2023

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.8k•0•0•0•Updated Jun 26, 2023Jun 26, 2023

    • WaIS

      Public
      Where is Insertion Sequence
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 6, 2022Dec 6, 2022

    • MGT_reads2alleles

      Public
      Pipeline for converting raw reads into alleles for submission to the MGT website
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Aug 10, 2022Aug 10, 2022

    • PhosSitesPerProtein

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 21, 2020Aug 21, 2020

    • MGT

      Public
      Multi-level Genome Typing
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Aug 12, 2019Aug 12, 2019

    • SnpFilt

      Public
      A package to identify SNPs using reference-free assembly
      Perl
      •
      GNU General Public License v3.0
      •3•3•1•0•Updated Aug 14, 2016Aug 14, 2016