BCCDC-PHL repositories

143 repositories

nfflu-results-collector
Public
Python
•1•2•0•0•Updated Sep 25, 2026Sep 25, 2026
determinator
Public
Sort fastqs or split reads based on competitive mapping to multiple references through bwa or bbsplit
Nextflow
•0•1•2•2•Updated Sep 25, 2026Sep 25, 2026
tbprofiler-nf
Public
Nextflow Wrapper for TBProfiler
bioinformatics-pipeline microbial-genomics tuberculosis-classification
bioinformatics-pipeline microbial-genomics tuberculosis-classification
Python
•2•4•4•0•Updated Sep 22, 2026Sep 22, 2026
amplicone
Public
Nextfllow pipeline for simulating amplicon-based sequencing reads using ART
Python
•
MIT License
•1•0•2•0•Updated Sep 17, 2026Sep 17, 2026
auto-cpo
Public
Automation of Genomic Analyses for Carbapenemase-Producing Organisms (CPOs)
automation microbial-genomics
automation microbial-genomics
Python
•
GNU General Public License v3.0
•0•0•5•1•Updated Sep 8, 2026Sep 8, 2026
autocycler-nf
Public
Nextflow implementation of the Autocycler long-read assembler
Nextflow
•0•1•0•0•Updated Sep 8, 2026Sep 8, 2026
basic-nanopore-qc
Public
Collect basic sequence QC metrics from nanopore reads
quality-control next-generation-sequencing microbial-genomics
quality-control next-generation-sequencing microbial-genomics
Nextflow
•
MIT License
•1•0•0•0•Updated Aug 27, 2026Aug 27, 2026
tick-COI-amplicon-illumina-nf
Public
Tick cytochrome oxidase subunit I (COI) amplicon sequencing
Python
•0•0•0•0•Updated Aug 26, 2026Aug 26, 2026
AMR-TB-amplicon-artic-nf
Public
Nextflow
•0•0•0•0•Updated Aug 21, 2026Aug 21, 2026
routine-sequence-qc
Public
Pipeline for running routine quality control analyses on illumina sequence data
bioinformatics quality-control next-generation-sequencing
bioinformatics quality-control next-generation-sequencing
Nextflow
•3•1•8•0•Updated Aug 11, 2026Aug 11, 2026
auto-routine-sequence-qc
Public
Python
•0•0•1•0•Updated Aug 6, 2026Aug 6, 2026
roary-nf
Public
Nextflow
•0•0•0•0•Updated Aug 1, 2026Aug 1, 2026
routine-sequence-qc-collector
Public
Collect outputs from BCCDC-PHL/routine-sequence-qc pipeline for usage by BCCDC-PHL/routine-sequence-qc-site
quality-control next-generation-sequencing microbial-genomics
quality-control next-generation-sequencing microbial-genomics data-management
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 28, 2026Jul 28, 2026
PCR_strainer
Public
A tool for assessing the inclusivity of primer and probe oligonucleotides from PCR assays against numerous reference genome sequences
Python
•
MIT License
•3•1•1•0•Updated Jul 21, 2026Jul 21, 2026
auspice
Public
Web app for visualizing pathogen evolution
JavaScript
•
GNU Affero General Public License v3.0
•172•0•0•0•Updated Jun 23, 2026Jun 23, 2026
routine-sequence-qc-site
Public
A site for displaying routine sequence QC data
quality-control clojurescript next-generation-sequencing
quality-control clojurescript next-generation-sequencing microbial-genomics
Clojure
•
GNU Affero General Public License v3.0
•0•0•1•0•Updated Jun 22, 2026Jun 22, 2026
auto-ncov
Public
Automated genomic analysis of SARS-CoV-2 sequence data
automation microbial-genomics genomic-epidemiology
automation microbial-genomics genomic-epidemiology
Python
•0•1•3•0•Updated Jun 22, 2026Jun 22, 2026
auto-illumina-run-qc-check
Public
Automated Primary Sequence QC Checks for Illumina Sequencing Runs
quality-control next-generation-sequencing laboratory-automation
quality-control next-generation-sequencing laboratory-automation
Python
•0•1•0•0•Updated Jun 19, 2026Jun 19, 2026
auto-hcv
Public
Automated genomic analysis of HCV sequence data
automation microbial-genomics
automation microbial-genomics
Python
•
MIT License
•1•0•0•0•Updated Jun 19, 2026Jun 19, 2026
symlink-seqs
Public
Create fastq symlinks for selected samples in sequencer output directories based on several criteria
next-generation-sequencing data-management illumina-sequencing
next-generation-sequencing data-management illumina-sequencing symlinks-manager
Python
•0•0•0•0•Updated Jun 18, 2026Jun 18, 2026
bdip-sheets-converter-site
Public
Web-based solution for preparing PulseNet metadata for input to BDIP Sheets
automation clojurescript static-site
automation clojurescript static-site data-cleaning
Clojure
•1•1•0•0•Updated Jun 5, 2026Jun 5, 2026
ncov-tools-nf
Public
A nextflow-based workflow for running ncov-tools
wrapper bioinformatics next-generation-sequencing
wrapper bioinformatics next-generation-sequencing quality-metrics covid-19 sars-cov-2
Nextflow
•4•2•1•0•Updated May 28, 2026May 28, 2026
ncov-tools
Public
Small collection of tools for performing quality control on coronavirus sequencing data and genomes
Python
•
MIT License
•15•0•3•1•Updated May 28, 2026May 28, 2026
wasteflow2
Public
Nextflow pipeline for probe-enriched pathogen surveillance in wastewater
Nextflow
•
MIT License
•0•0•2•1•Updated May 26, 2026May 26, 2026
hcv-nf
Public
Genomic analysis pipeline for genotyping of Hepatitis C Virus
next-generation-sequencing microbial-genomics data-analysis-pipeline
next-generation-sequencing microbial-genomics data-analysis-pipeline hepatitis-c-virus
Python
•
MIT License
•0•2•0•1•Updated May 6, 2026May 6, 2026
routine-assembly
Public
Pipeline for performing routine genome assembly
bioinformatics-pipeline genome-annotation genome-assembly
bioinformatics-pipeline genome-annotation genome-assembly
Nextflow
•2•3•7•0•Updated Apr 30, 2026Apr 30, 2026
pangolin-nf
Public
Run pangolin on multiple output directories from BCCDC-PHL/ncov2019-artic-nf
bioinformatics sars-cov-2 lineages
bioinformatics sars-cov-2 lineages
Nextflow
•0•1•2•0•Updated Apr 13, 2026Apr 13, 2026
ncov2019-artic-nf
Public
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Nextflow
•87•4•4•1•Updated Apr 10, 2026Apr 10, 2026
riboscope
Public
Scoping prokaryotic ribosomal repeat regions for SNVs from short paired-end sequences.
HTML
•
Apache License 2.0
•0•0•0•0•Updated Mar 31, 2026Mar 31, 2026
covflo
Public
Nextflow pipeline for generation of BCCDC routine SARS-CoV-2 phylogenetic trees to be visualized with Auspice.
nextflow phylogenetics trees
nextflow phylogenetics trees viral evolutionary nextstrain auspice sars-cov-2 microbe
Python
•
GNU General Public License v3.0
•3•3•0•0•Updated Mar 25, 2026Mar 25, 2026

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BC Centre for Disease Control Public Health Laboratory

All

143 repositories

nfflu-results-collector

determinator

tbprofiler-nf

amplicone

auto-cpo

autocycler-nf

basic-nanopore-qc

tick-COI-amplicon-illumina-nf

AMR-TB-amplicon-artic-nf

routine-sequence-qc

auto-routine-sequence-qc

roary-nf

routine-sequence-qc-collector

PCR_strainer

auspice

routine-sequence-qc-site

auto-ncov

auto-illumina-run-qc-check

auto-hcv

symlink-seqs

bdip-sheets-converter-site

ncov-tools-nf

ncov-tools

wasteflow2

hcv-nf

routine-assembly

pangolin-nf

ncov2019-artic-nf

riboscope

covflo

Repositories list

143 repositories