Skip to content

@pathogenwatch-oss pathogenwatch-oss

Change the repository type filter

All

    Repositories list

    21 repositories

    • website

      Public
      The main website code for Pathogenwatch
      JavaScript
      •
      MIT License
      •0•2•0•0•Updated Oct 17, 2024Oct 17, 2024

    • tasks

      Public
      The Pathogenwatch task image build scripts.
      JavaScript
      •0•0•0•0•Updated Oct 16, 2024Oct 16, 2024

    • kleborate

      Public
      The Pathogenwatch wrapper for Kleborate
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • hclink

      Public
      Link Pathogenwatch cgMLST profile to Enterobase HierCC clusters
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

    • typing-databases

      Public
      The scripts for creating the typing database used by the MLST code.
      Shell
      •0•1•0•0•Updated Jun 17, 2024Jun 17, 2024

    • mlst

      Public
      The Pathogenwatch MLST/cgMLST assignment tool
      JavaScript
      •0•4•0•0•Updated Jun 14, 2024Jun 14, 2024

    • poppunk2

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 3, 2024Jun 3, 2024

    • core-fp

      Public
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Apr 18, 2024Apr 18, 2024

    • cgmlst-clustering

      Public
      Go
      •
      MIT License
      •0•0•0•0•Updated Apr 4, 2024Apr 4, 2024

    • amr-search

      Public
      The Pathogenwatch AMR genotyping and phenotype inference tool
      Java
      •
      MIT License
      •1•0•0•0•Updated Sep 18, 2023Sep 18, 2023

    • amr-libraries

      Public
      The CGPS curated AMR libraries used by Pathogenwatch
      MIT License
      •0•0•0•0•Updated Sep 18, 2023Sep 18, 2023

    • amr-test-libraries

      Public
      AMR libraries that haven't yet met production-ready standards for Pathogenwatch.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 18, 2023Sep 18, 2023

    • vista

      Public
      The Pathogenwatch Vibrio cholerae genotyping tool
      Python
      •
      MIT License
      •0•5•0•0•Updated Sep 8, 2023Sep 8, 2023

    • support

      Public
      About Pathogenwatch-OSS
      0•0•0•0•Updated Jul 11, 2023Jul 11, 2023

    • speciator

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 10, 2023Mar 10, 2023

    • inctyper

      Public
      The Pathogenwatch inctyping tool, based on plasmidfinder
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 18, 2023Jan 18, 2023

    • spn-resistance-pbp

      Public
      PBP resistance assignment for Streptococcus pneumoniae
      Perl
      •
      MIT License
      •1•0•0•0•Updated Jan 12, 2023Jan 12, 2023

    • genotyphi

      Public
      Pathogenwatch implementation of the Genotyphi tool
      Java
      •
      MIT License
      •0•0•0•0•Updated Dec 20, 2022Dec 20, 2022

    • ngono-markers

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 28, 2022Sep 28, 2022

    • seroba

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 26, 2022Sep 26, 2022

    • pw-bactinspector

      Public
      The Pathogenwatch fork of bactinspector that is Speciator 3.
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 26, 2022Sep 26, 2022