BC Centre for Disease Control Public Health Laboratory
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auto-routine-nanopore-qc
Public- Create fastq symlinks for selected samples in sequencer output directories based on several criteria
bioinflow
Publicauto-pangolin
Publicauto-ncov
PublicAutomated genomic analysis of SARS-CoV-2 sequence datancov2019-artic-nf
PublicA Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019auto-tb-amr-amplicon
Publicauto-cpo
PublicAutomation of Genomic Analyses for Carbapenemase-Producing Organisms (CPOs)auto-routine-sequence-qc
Public- Pipeline for running routine quality control analyses on illumina sequence data
plasmid-assembly
Publiccluster-plasmids
PublicA workflow for assessing similarity between a set of plasmid sequencescpo-results-collector
Publicmpxv-qc
PublicWasteFlow
PublicNextflow pipeline for pathogen surveillance in wastewatercovid-qc-collector
Publiccovid-qc
PublicStatic site for displaying COVID-19 sequencing quality control datataxon-abundance
Publicfluviewer-nf
Public- Pipeline for performing routine genome assembly
auto-fastq-symlink
PublicAutomated symlinking of sequence datadownsample-reads
Publicmlst-nf
PublicRun mlst on multiple samples with integrated quality control.tbprofiler-nf
PublicNextflow Wrapper for TBProfilerkma-cgmlst
PublicA cgMLST pipeline based on the KMA alignerroary-nf
Publicamplicone
Publiccgmlst-clustering
PublicScripts to support clustering of cgMLST allele profiles