BC Centre for Disease Control Public Health Laboratory
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121 repositories
fluflo
PublicNextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.plasmid-assembly
Publictbprofiler-nf
PublicNextflow Wrapper for TBProfilersnippy-variants
PublicPerform read mapping and variant calling using snippyfluviewer-nf
Publicmpxv-artic-nf
Publicprocess-nanopore
Publicauspice-docker
Publicauspice
Publicnorovirus-blast-nf
Publicamplicone
Publiccpo-results-collector
Publicbasic-sequence-qc
PublicGenerate some basic quality control statistics on an arbitrary set of illumina fastq sequence files.amplicon-consensus
Publicalignment-variants
PublicPipeline to perform alignment & variant calling on whole-genome sequence dataartic-mpxv2022
Publicauto-ncov
PublicAutomated genomic analysis of SARS-CoV-2 sequence datanextclade-nf
Publicdemultiplex-nanopore
PublicDemultiplex nanopore reads and combine into a single file per sampleWasteFlow
PublicNextflow pipeline for pathogen surveillance in wastewaterauto-cpo
PublicAutomation of Genomic Analyses for Carbapenemase-Producing Organisms (CPOs)- Remove host reads from a microbial pathogen sequence dataset by aligning against a reference genome. Verify that the reads were removed using Kraken2/Bracken
symlink-seqs
PublicCreate fastq symlinks for selected samples in sequencer output directories based on several criteriakma-cgmlst
PublicA cgMLST pipeline based on the KMA alignerFluViewer
PublicTool for generating influenza A virus genome sequences from FASTQ datanfvibrio
Publicauto-flu
Publicnoro-phylo-nf
Publicroutine-sequence-qc-site
PublicA site for displaying routine sequence QC data- Automated Primary Sequence QC Checks for Illumina Sequencing Runs