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/fluflo
Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.
BCCDC-PHL/simulate-short-reads
Generate simulated illumina sequence reads from a reference sequence
BCCDC-PHL/taxon-abundance
BCCDC-PHL/covid-qc
Static site for displaying COVID-19 sequencing quality control data
BCCDC-PHL/simulate-long-reads
Generate simulated oxford nanopore reads from a reference sequence
BCCDC-PHL/cgmlst-clustering
Scripts to support clustering of cgMLST allele profiles
BCCDC-PHL/covflo
Nextflow pipeline for generation of BCCDC routine SARS-CoV-2 phylogenetic trees to be visualized with Auspice.
BCCDC-PHL/ncov-tools-nf
A nextflow-based workflow for running ncov-tools
BCCDC-PHL/auto-fastq-symlink
Automated symlinking of sequence data
BCCDC-PHL/mlst-nf
Run mlst on multiple samples with integrated quality control.
BCCDC-PHL/snippy-core-phylogenomics
BCCDC-PHL/amplicone
BCCDC-PHL/auto-irida-azure-upload
Automated upload of sequence data to IRIDA platform
BCCDC-PHL/auto-irida-uploader
Automated uploading of sequence data into IRIDA instances, used in conjunction with auto-irida-azure-upload
BCCDC-PHL/auto-routine-sequence-qc
BCCDC-PHL/covid-qc-collector
BCCDC-PHL/cpo-qc-collector
Collect QC data from Carbapenemase-Producing Organism (CPO) genomic analyses
BCCDC-PHL/downsample-reads
Downsample fastq reads for mutiple samples, at multiple depths
BCCDC-PHL/flu-helper-scripts
A set of scripts for working with Influenza data
BCCDC-PHL/ncov-tools
Small collection of tools for performing quality control on coronavirus sequencing data and genomes
BCCDC-PHL/nextclade-generator
A repository dedicated to the generation of a novel Nextclade dataset for the H5NX subtypes of Influenza A.
BCCDC-PHL/norovirus-blast-analysis-site
BCCDC-PHL/norovirus-blast-nf
nextflow wrapper for noroblast
BCCDC-PHL/PCR_strainer
A tool for assessing the inclusivity of primer and probe oligonucleotides from PCR assays against numerous reference genome sequences
BCCDC-PHL/pipeline-provenance-schema
BCCDC-PHL/plasmid-assembly
BCCDC-PHL/referenceseeker-nf
Simple Nextflow wrapper for running ReferenceSeeker with integrated QC.
BCCDC-PHL/routine-sequence-qc-collector
Collect outputs from BCCDC-PHL/routine-sequence-qc pipeline for usage by BCCDC-PHL/routine-sequence-qc-site
BCCDC-PHL/sequencing-runs-collector-illumina
A service for storing and retrieving info about sequencing runs.
BCCDC-PHL/snippy-variants
Perform read mapping and variant calling using snippy