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/simulate-short-reads
Generate simulated illumina sequence reads from a reference sequence
BCCDC-PHL/dragonflye-nf
Nextflow wrapper for the dragonflye assembler, with additional QC
BCCDC-PHL/simulate-long-reads
Generate simulated oxford nanopore reads from a reference sequence
BCCDC-PHL/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
BCCDC-PHL/tb-db
Database for storage of M. tuberculosis genomics analysis results
BCCDC-PHL/vcf-diff
Check for differences between two vcf files
BCCDC-PHL/blast-reads
BLAST a set of fastq reads against a database
BCCDC-PHL/degrade-fastq
A tool for artificially degrading the quality of fastq files
BCCDC-PHL/hcv-nf
Genomic analysis pipeline for genotyping of Hepatitis C Virus
BCCDC-PHL/pangolin-nf
Run pangolin on multiple output directories from BCCDC-PHL/ncov2019-artic-nf
BCCDC-PHL/routine-sequence-qc
Pipeline for running routine quality control analyses on illumina sequence data
BCCDC-PHL/abritamr
A pipeline for running AMRfinderPlus and collating results into functional classes
BCCDC-PHL/align-compare
Pipeline to make pairwise comparisons of matched fasta sequences.
BCCDC-PHL/auto-pangolin
Automated lineage assignment of SARS-CoV-2 sequences with pangolin
BCCDC-PHL/auto-routine-nanopore-qc
BCCDC-PHL/auto-routine-sequence-qc
BCCDC-PHL/basic-nanopore-qc
Collect basic sequence QC metrics from nanopore reads
BCCDC-PHL/cluster-plasmids
A workflow for assessing similarity between a set of plasmid sequences
BCCDC-PHL/emmtyper
emm Automatic Isolate Labeller
BCCDC-PHL/fasta-blasta
BCCDC-PHL/FluViewer-db
BCCDC-PHL/irida-upload-monitor-collector
Collect info about IRIDA uploads for display in monitoring site
BCCDC-PHL/irida-upload-monitor-site
Site for monitoring IRIDA uploads
BCCDC-PHL/ncov-recombinant
Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
BCCDC-PHL/ncov-recombinant-nf
Nextflow wrapper for ktmeaton/ncov-recombinant
BCCDC-PHL/norovirus-blast-analysis-site
BCCDC-PHL/referenceseeker-nf
Simple Nextflow wrapper for running ReferenceSeeker with integrated QC.
BCCDC-PHL/routine-nanopore-qc
Routine sequence QC for nanopore data
BCCDC-PHL/routine-nanopore-qc-collector
Collect Routine QC for Nanopore Sequence Data
BCCDC-PHL/sequencing-runs-service
A web service for providing info about sequencing runs.