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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 190 30

  2. mob-suite mob-suite Public

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

    Python 171 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

    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
  • irida-next Public

    IRIDA Next

    phac-nml/irida-next’s past year of commit activity
    Ruby 13 Apache-2.0 3 5 20 Updated Mar 16, 2026
  • galaxy_tools Public

    Contains a set of Galaxy Tools mostly written by the Bioinformatics core at NML

    phac-nml/galaxy_tools’s past year of commit activity
    Perl 16 Apache-2.0 26 9 15 Updated Mar 16, 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 14, 2026
  • nf-ViralMutations Public

    Generic pipeline for calling mutations against a viral reference genome

    phac-nml/nf-ViralMutations’s past year of commit activity
    Nextflow 1 Apache-2.0 1 8 0 Updated Mar 13, 2026
  • measeq Public

    Measles Sequence Analysis and Automation

    phac-nml/measeq’s past year of commit activity
    Nextflow 5 MIT 1 0 1 Updated Mar 13, 2026
  • staramrnf Public

    nf-core StarAMR

    phac-nml/staramrnf’s past year of commit activity
    Nextflow 0 MIT 1 2 0 Updated Mar 13, 2026
  • submitdatairidanext Public

    Pipeline for submitting data to INSDC databases for IRIDA Next

    phac-nml/submitdatairidanext’s past year of commit activity
    Nextflow 1 MIT 0 2 0 Updated Mar 12, 2026
  • mikrokondo Public

    A simple pipeline for bacterial assembly and quality control

    phac-nml/mikrokondo’s past year of commit activity
    Nextflow 16 MIT 4 19 1 Updated Mar 12, 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 4 5 0 Updated Mar 10, 2026
  • genomic_address_service Public

    Package for clustering sequences de novo and assignment to existing nomenclature

    phac-nml/genomic_address_service’s past year of commit activity
    Python 1 Apache-2.0 4 14 1 Updated Mar 10, 2026

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