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@phac-nml

National Microbiology Laboratory

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  1. staramr staramr Public

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

    Python 136 28

  2. mob-suite mob-suite Public

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

    Python 135 32

  3. ecoli_serotyping ecoli_serotyping Public

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

    Python 51 11

  4. refseq_masher refseq_masher Public

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

    Jupyter Notebook 41 4

  5. irida irida Public

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

    Java 40 31

  6. sistr_cmd sistr_cmd Public

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

    Python 27 9

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 11 Updated Mar 1, 2025
  • fetchdatairidanext Public

    Pipeline for downloading data from INSDC databases for IRIDA Next.

    phac-nml/fetchdatairidanext’s past year of commit activity
    Nextflow 0 MIT 2 2 0 Updated Feb 28, 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 Feb 28, 2025
  • gasnomenclature Public

    Nomenclature assignment pipeline

    phac-nml/gasnomenclature’s past year of commit activity
    Nextflow 0 MIT 1 3 2 Updated Feb 28, 2025
  • mikrokondo Public

    A simple pipeline for bacterial assembly and quality control

    phac-nml/mikrokondo’s past year of commit activity
    Nextflow 16 MIT 3 24 4 Updated Feb 28, 2025
  • locidex Public

    Common search engine for similarity based typing applications

    phac-nml/locidex’s past year of commit activity
    Python 4 MIT 0 13 1 Updated Feb 28, 2025
  • phac-nml/metadatatransformation’s past year of commit activity
    Nextflow 0 MIT 0 1 0 Updated Feb 27, 2025
  • 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 0 0 Updated Feb 27, 2025
  • arboratornf Public

    EPS suite Arborator pipeline

    phac-nml/arboratornf’s past year of commit activity
    Nextflow 0 MIT 0 3 0 Updated Feb 27, 2025
  • staramrnf Public

    nf-core StarAMR

    phac-nml/staramrnf’s past year of commit activity
    Nextflow 0 MIT 1 2 1 Updated Feb 27, 2025

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