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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 141 28

  2. mob-suite mob-suite Public

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

    Python 140 32

  3. ecoli_serotyping ecoli_serotyping Public

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

    Python 52 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 151 repositories
  • irida-next Public

    IRIDA Next

    phac-nml/irida-next’s past year of commit activity
    Ruby 9 Apache-2.0 3 15 10 Updated Mar 24, 2025
  • typingQC Public

    Genotyping Quality Control (typingQC)

    phac-nml/typingQC’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Mar 24, 2025
  • mpox-resources Public

    Resources and tutorials related to Mpox analyses.

    phac-nml/mpox-resources’s past year of commit activity
    0 Apache-2.0 0 0 0 Updated Mar 24, 2025
  • sistr_cmd Public

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

    phac-nml/sistr_cmd’s past year of commit activity
    Python 27 Apache-2.0 9 10 (1 issue needs help) 0 Updated Mar 24, 2025
  • venae Public

    A workflow to rapidly identify species and antimicrobial resistance genes in positive blood cultures sequenced using Oxford Nanopore Technologies (ONT)

    phac-nml/venae’s past year of commit activity
    HTML 0 Apache-2.0 0 0 0 Updated Mar 24, 2025
  • pangwas Public

    A pipeline for pangenome wide association studies (panGWAS).

    phac-nml/pangwas’s past year of commit activity
    Python 1 Apache-2.0 0 8 0 Updated Mar 24, 2025
  • ArborView Public

    A way to visualize beautiful phylogenetic trees alongside contextual data.

    phac-nml/ArborView’s past year of commit activity
    HTML 1 0 1 1 Updated Mar 21, 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 4 12 2 Updated Mar 21, 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 Mar 20, 2025
  • staramrnf Public

    nf-core StarAMR

    phac-nml/staramrnf’s past year of commit activity
    Nextflow 0 MIT 1 2 0 Updated Mar 20, 2025