BC Centre for Disease Control Public Health Laboratory

fluflo

Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.

bioinflow

Nextflow pipeline for providing public health bioinfo.

taxon-abundance

WasteFlow

Nextflow pipeline for pathogen surveillance in wastewater

kma-cgmlst

A cgMLST pipeline based on the KMA aligner

simulate-long-reads

Generate simulated oxford nanopore reads from a reference sequence

tbprofiler-nf

Nextflow Wrapper for TBProfiler

cgmlst-clustering

Scripts to support clustering of cgMLST allele profiles

mpxv-artic-nf

auto-fastq-symlink

Automated symlinking of sequence data

basic-sequence-qc

Generate some basic quality control statistics on an arbitrary set of illumina fastq sequence files.

mlst-nf

Run mlst on multiple samples with integrated quality control.

routine-assembly

Pipeline for performing routine genome assembly

snippy-core-phylogenomics

alignment-variants

Pipeline to perform alignment & variant calling on whole-genome sequence data

amplicon-consensus

amplicone

auspice

Web app for visualizing pathogen evolution

auspice-docker

auto-routine-nanopore-qc

cpo-results-collector

downsample-reads

Downsample fastq reads for mutiple samples, at multiple depths

fluviewer-nf

Nextflow pipeline for influenza A whole genome sequence analysis

norovirus-blast-nf

nextflow wrapper for noroblast

plasmid-assembly

process-nanopore

A pipeline for processing raw sequence data from nanopore runs

roary-nf

routine-nanopore-qc

Routine sequence QC for nanopore data

routine-nanopore-qc-collector

Collect Routine QC for Nanopore Sequence Data

snippy-variants

Perform read mapping and variant calling using snippy