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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.

Pinned

  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 2 1

  2. illumina-uploader illumina-uploader Public

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

    Python 2 1

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

    Python 1 1

  4. covid-qc covid-qc Public

    Static site for displaying COVID-19 sequencing quality control data

    Clojure 3

Repositories

Showing 10 of 119 repositories
  • cpo-results-collector Public
    BCCDC-PHL/cpo-results-collector’s past year of commit activity
    Python 0 0 3 0 Updated Aug 16, 2024
  • nextclade-nf Public

    Pipeline for running nextclade

    BCCDC-PHL/nextclade-nf’s past year of commit activity
    Nextflow 0 0 0 0 Updated Aug 14, 2024
  • fluviewer-nf Public

    Nextflow pipeline for influenza A whole genome sequence analysis

    BCCDC-PHL/fluviewer-nf’s past year of commit activity
    Nextflow 0 0 4 1 Updated Aug 9, 2024
  • tbprofiler-nf Public

    Nextflow Wrapper for TBProfiler

    BCCDC-PHL/tbprofiler-nf’s past year of commit activity
    Python 4 2 2 1 Updated Aug 3, 2024
  • demultiplex-nanopore Public

    Demultiplex nanopore reads and combine into a single file per sample

    BCCDC-PHL/demultiplex-nanopore’s past year of commit activity
    Nextflow 1 0 0 0 Updated Jul 31, 2024
  • WasteFlow Public

    Nextflow pipeline for pathogen surveillance in wastewater

    BCCDC-PHL/WasteFlow’s past year of commit activity
    Nextflow 4 GPL-3.0 0 0 0 Updated Jul 30, 2024
  • auto-cpo Public

    Automation of Genomic Analyses for Carbapenemase-Producing Organisms (CPOs)

    BCCDC-PHL/auto-cpo’s past year of commit activity
    Python 0 GPL-3.0 0 5 0 Updated Jul 30, 2024
  • dehost-and-verify-illumina Public

    Remove host reads from a microbial pathogen sequence dataset by aligning against a reference genome. Verify that the reads were removed using Kraken2/Bracken

    BCCDC-PHL/dehost-and-verify-illumina’s past year of commit activity
    Nextflow 1 0 3 0 Updated Jul 23, 2024
  • symlink-seqs Public

    Create fastq symlinks for selected samples in sequencer output directories based on several criteria

    BCCDC-PHL/symlink-seqs’s past year of commit activity
    Python 0 0 2 0 Updated Jul 23, 2024
  • kma-cgmlst Public

    A cgMLST pipeline based on the KMA aligner

    BCCDC-PHL/kma-cgmlst’s past year of commit activity
    Nextflow 3 MIT 1 3 0 Updated Jul 22, 2024
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