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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 142 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 53 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 152 repositories
  • irida-next Public

    IRIDA Next

    Ruby 9 Apache-2.0 3 17 10 Updated Mar 27, 2025
  • sequenoscope Public

    A set of tools designed for ONT sequencing analysis, enabling the exploration and comparison of sequencing outcomes across experimental conditions.

    Python 5 1 0 0 Updated Mar 26, 2025
  • genomic_address_service Public

    Package for clustering sequences de novo and assignment to existing nomenclature

    Python 1 Apache-2.0 4 12 2 Updated Mar 26, 2025
  • irida-plugin-sistr Public

    IRIDA Plugin for SISTR Salmonella Typing Tool

    Java 0 0 2 0 Updated Mar 26, 2025
  • Shell 0 Apache-2.0 1 0 0 Updated Mar 26, 2025
  • pangwas Public

    A pipeline for pangenome wide association studies (panGWAS).

    Python 1 Apache-2.0 0 8 0 Updated Mar 25, 2025
  • mpox-resources Public

    Resources and tutorials related to Mpox analyses.

    0 Apache-2.0 0 0 0 Updated Mar 25, 2025
  • profile_dists Public

    Profile Dists: Convenient package for comparing genetic similarity of samples based on allelic profiles

    Python 2 Apache-2.0 1 6 1 Updated Mar 25, 2025
  • typingQC Public

    Genotyping Quality Control (typingQC)

    Nextflow 0 MIT 0 0 0 Updated Mar 25, 2025
  • sistr_cmd Public

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

    Python 27 Apache-2.0 9 10 (1 issue needs help) 0 Updated Mar 24, 2025

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