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National Microbiology Laboratory

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  1. staramr staramr Public

    Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

    Python 193 30

  2. mob-suite mob-suite Public

    MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

    Python 172 33

  3. ecoli_serotyping ecoli_serotyping Public

    In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping

    Python 65 11

  4. irida irida Public

    ⛔️ DEPRECATED Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology

    Java 43 33

  5. refseq_masher refseq_masher Public

    Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database

    Jupyter Notebook 43 4

  6. sistr_cmd sistr_cmd Public

    SISTR (Salmonella In Silico Typing Resource) command-line tool

    Python 33 10

Repositories

Showing 10 of 162 repositories
  • fastmatchirida Public

    Quickly refines a reference set of samples based on distance.

    phac-nml/fastmatchirida’s past year of commit activity
    Nextflow 1 MIT 0 1 0 Updated Mar 30, 2026
  • irida-next Public

    IRIDA Next

    phac-nml/irida-next’s past year of commit activity
    Ruby 13 Apache-2.0 3 5 29 Updated Mar 30, 2026
  • viralassembly Public

    Assemble and QC viral reads with a reference scheme

    phac-nml/viralassembly’s past year of commit activity
    Nextflow 1 MIT 1 0 2 Updated Mar 30, 2026
  • asipython Public

    Python library that calculates viral drug resistance interpretations/scores based on given algorithm and mutation list files

    phac-nml/asipython’s past year of commit activity
    Python 1 Apache-2.0 0 0 2 Updated Mar 30, 2026
  • irida-plugin-amr-detection Public

    IRIDA Plugin for AMR Detection

    phac-nml/irida-plugin-amr-detection’s past year of commit activity
    Java 2 Apache-2.0 3 6 1 Updated Mar 27, 2026
  • irida-plugin-example Public

    An example pipeline plugin for IRIDA.

    phac-nml/irida-plugin-example’s past year of commit activity
    Java 0 Apache-2.0 1 0 1 Updated Mar 27, 2026
  • irida-plugin-ectyper Public

    IRIDA plugin for ECTyper (E.coli in silico typing tool)

    phac-nml/irida-plugin-ectyper’s past year of commit activity
    Java 2 0 0 1 Updated Mar 27, 2026
  • arboratornf Public

    EPS suite Arborator pipeline

    phac-nml/arboratornf’s past year of commit activity
    Nextflow 0 MIT 0 8 0 Updated Mar 27, 2026
  • pathogen-view-components Public

    Rails ViewComponent gem providing accessible, i18n-ready UI components with Stimulus controllers, built by the Public Health Agency of Canada's Bioinformatics team

    phac-nml/pathogen-view-components’s past year of commit activity
    HTML 0 Apache-2.0 0 0 3 Updated Mar 27, 2026
  • legiovue Public

    A nextflow pipeline for whole-genome analysis of *Legionella pneumophila*

    phac-nml/legiovue’s past year of commit activity
    Nextflow 4 MIT 5 6 1 Updated Mar 27, 2026

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