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.
Vancouver, BC
Pinned Repositories
covid-qc
Static site for displaying COVID-19 sequencing quality control data
fluflo
Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.
FluViewer
Tool for generating influenza A virus genome sequences from FASTQ data
illumina-uploader
Watch for new files in Illumina sequencer and upload to remote server
mpxv-artic-nf
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
simulate-short-reads
Generate simulated illumina sequence reads from a reference sequence
taxon-abundance
tbprofiler-nf
Nextflow Wrapper for TBProfiler
WasteFlow
Nextflow pipeline for pathogen surveillance in wastewater
BC Centre for Disease Control Public Health Laboratory's Repositories
BCCDC-PHL/WasteFlow
Nextflow pipeline for pathogen surveillance in wastewater
BCCDC-PHL/FluViewer
Tool for generating influenza A virus genome sequences from FASTQ data
BCCDC-PHL/tbprofiler-nf
Nextflow Wrapper for TBProfiler
BCCDC-PHL/illumina-uploader
Watch for new files in Illumina sequencer and upload to remote server
BCCDC-PHL/kma-cgmlst
A cgMLST pipeline based on the KMA aligner
BCCDC-PHL/16s-nf
Prepare a report for taxonomic assignment based on 16S rRNA sequences, using BLAST.
BCCDC-PHL/mpxv-artic-nf
BCCDC-PHL/auto-flu
Automated analysis of flu sequence data using BCCDC-PHL/fluviewer-nf
BCCDC-PHL/auto-illumina-run-qc-check
Automated Primary Sequence QC Checks for Illumina Sequencing Runs
BCCDC-PHL/auto-ncov
Automated genomic analysis of SARS-CoV-2 sequence data
BCCDC-PHL/basic-sequence-qc
Generate some basic quality control statistics on an arbitrary set of illumina fastq sequence files.
BCCDC-PHL/dehost-and-verify-illumina
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/demultiplex-nanopore
Demultiplex nanopore reads and combine into a single file per sample
BCCDC-PHL/nfvibrio
Nextflow pipeline to run metagenomic sequence analysis of Vibrio Parahaemolyticus, based on nf-core template, by John Palmer & Zohaib Anwar
BCCDC-PHL/plasmid-screen
Screen plasmids for carbapenemase resistance genes, and classify using MOB Suite
BCCDC-PHL/alignment-variants
Pipeline to perform alignment & variant calling on whole-genome sequence data
BCCDC-PHL/amplicon-consensus
BCCDC-PHL/artic-mpxv2022
BCCDC-PHL/auspice
Web app for visualizing pathogen evolution
BCCDC-PHL/auspice-docker
BCCDC-PHL/auto-cpo
Automation of Genomic Analyses for Carbapenemase-Producing Organisms (CPOs)
BCCDC-PHL/auto-hcv
Automated genomic analysis of HCV sequence data
BCCDC-PHL/cpo-results-collector
BCCDC-PHL/fluviewer-nf
Nextflow pipeline for influenza A whole genome sequence analysis
BCCDC-PHL/nextclade-nf
Pipeline for running nextclade
BCCDC-PHL/noro-phylo-nf
Pipeline for performing multiple sequence alignment and phylogenetic tree reconstruction on norovirus sequence data.
BCCDC-PHL/noro-typing-nf
Norovirus metagenomics Nextflow pipeline
BCCDC-PHL/norovirus-blast-nf
nextflow wrapper for noroblast
BCCDC-PHL/routine-sequence-qc-site
A site for displaying routine sequence QC data
BCCDC-PHL/symlink-seqs
Create fastq symlinks for selected samples in sequencer output directories based on several criteria