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National Microbiology Laboratory

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  1. mob-suite mob-suite Public

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

    Python 134 32

  2. staramr staramr Public

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

    Python 127 28

  3. ecoli_serotyping ecoli_serotyping Public

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

    Python 51 11

  4. irida irida Public

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

    Java 40 31

  5. refseq_masher refseq_masher Public

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

    Jupyter Notebook 40 4

  6. biohansel biohansel Public

    Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes

    Python 27 7

Repositories

Showing 10 of 146 repositories
  • irida-next Public

    IRIDA Next

    phac-nml/irida-next’s past year of commit activity
    Ruby 9 Apache-2.0 3 15 9 Updated Feb 1, 2025
  • CryptoGenotyper Public

    CryptoGenotyper is a tool that allows for subtyping the parasite, Cryptosporidium

    phac-nml/CryptoGenotyper’s past year of commit activity
    Python 0 1 4 0 Updated Jan 31, 2025
  • legiovue Public

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

    phac-nml/legiovue’s past year of commit activity
    Nextflow 1 MIT 2 4 0 Updated Jan 31, 2025
  • pipeline-standards Public

    Guidelines for developing Nextflow pipelines for IRIDA Next.

    phac-nml/pipeline-standards’s past year of commit activity
    2 Apache-2.0 1 7 0 Updated Jan 31, 2025
  • 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 3 8 0 Updated Jan 31, 2025
  • nf-iridanext Public

    Plugin for integration of Nextflow pipelines with IRIDA Next.

    phac-nml/nf-iridanext’s past year of commit activity
    Groovy 5 Apache-2.0 0 5 0 Updated Jan 31, 2025
  • irida Public

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

    phac-nml/irida’s past year of commit activity
    Java 40 Apache-2.0 31 169 8 Updated Jan 31, 2025
  • phac-nml/metadatatransformation’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Jan 30, 2025
  • 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 0 Updated Jan 30, 2025
  • gasnomenclature Public

    Nomenclature assignment pipeline

    phac-nml/gasnomenclature’s past year of commit activity
    Nextflow 0 MIT 0 5 1 Updated Jan 29, 2025