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@BCCDC-PHL

BC Centre for Disease Control Public Health Laboratory

The BCCDC Public Health Laboratory is the primary public health and reference diagnostic testing facility for British Columbia.

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  1. ncov2019-artic-nf ncov2019-artic-nf Public

    Forked from connor-lab/ncov2019-artic-nf

    A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

    Nextflow 4 1

  2. illumina-uploader illumina-uploader Public

    Watch for new files in Illumina sequencer and upload to remote server

    Python 4 1

  3. mpxv-artic-nf mpxv-artic-nf Public

    Nextflow 3 4

  4. covid-qc covid-qc Public

    Static site for displaying COVID-19 sequencing quality control data

    Clojure 5

Repositories

Showing 10 of 134 repositories
  • covflo Public

    Nextflow pipeline for generation of BCCDC routine SARS-CoV-2 phylogenetic trees to be visualized with Auspice.

    BCCDC-PHL/covflo’s past year of commit activity
    Python 2 GPL-3.0 3 0 0 Updated Mar 25, 2026
  • wasteflow2 Public

    Nextflow pipeline for probe-enriched pathogen surveillance in wastewater

    BCCDC-PHL/wasteflow2’s past year of commit activity
    Nextflow 0 MIT 0 2 1 Updated Mar 10, 2026
  • tick-COI-amplicon-illumina-nf Public

    Tick cytochrome oxidase subunit I (COI) amplicon sequencing

    BCCDC-PHL/tick-COI-amplicon-illumina-nf’s past year of commit activity
    Python 0 0 0 0 Updated Mar 5, 2026
  • routine-assembly Public

    Pipeline for performing routine genome assembly

    BCCDC-PHL/routine-assembly’s past year of commit activity
    Nextflow 2 2 6 0 Updated Mar 3, 2026
  • illumina-uploader Public

    Watch for new files in Illumina sequencer and upload to remote server

    BCCDC-PHL/illumina-uploader’s past year of commit activity
    Python 4 1 3 0 Updated Feb 26, 2026
  • nf-shovill Public

    a nextflow wrapper for shovill

    BCCDC-PHL/nf-shovill’s past year of commit activity
    Nextflow 0 0 0 0 Updated Feb 4, 2026
  • abricate-nf Public

    A Nextflow pipeline to run the Abricate tool by Torsten Seemann compliant with BCCDC workflow standards

    BCCDC-PHL/abricate-nf’s past year of commit activity
    Nextflow 0 0 0 0 Updated Feb 3, 2026
  • mlst-nf Public

    Run mlst on multiple samples with integrated quality control.

    BCCDC-PHL/mlst-nf’s past year of commit activity
    Nextflow 2 1 3 0 Updated Feb 3, 2026
  • referenceseeker-nf Public

    Simple Nextflow wrapper for running ReferenceSeeker with integrated QC.

    BCCDC-PHL/referenceseeker-nf’s past year of commit activity
    Nextflow 0 0 0 0 Updated Jan 30, 2026
  • auspice Public Forked from nextstrain/auspice

    Web app for visualizing pathogen evolution

    BCCDC-PHL/auspice’s past year of commit activity
    JavaScript 0 AGPL-3.0 172 0 0 Updated Jan 12, 2026
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