Repositories list

• hcv-nf

  Public
  Genomic analysis pipeline for genotyping of Hepatitis C Virus

  next-generation-sequencingmicrobial-genomicsdata-analysis-pipeline+ 1hepatitis-c-virus

  Python

  •

  MIT License

  •0•1•0•0•Updated Oct 30, 2025Oct 30, 2025

• downsample-reads

  Public
  Downsample fastq reads for mutiple samples, at multiple depths

  Nextflow

  •1•0•2•0•Updated Oct 24, 2025Oct 24, 2025

• snippy-variants

  Public
  Perform read mapping and variant calling using snippy

  microbial-genomicsvariant-calling

  Nextflow

  •1•0•4•3•Updated Oct 21, 2025Oct 21, 2025

• cutadapt-nf

  Public
  Nextflow

  •0•0•0•0•Updated Oct 15, 2025Oct 15, 2025

• auto-hcv

  Public
  Automated genomic analysis of HCV sequence data

  automationmicrobial-genomics

  Python

  •

  MIT License

  •1•0•0•0•Updated Oct 15, 2025Oct 15, 2025

• auto-irida-uploader

  Public
  Automated uploading of sequence data into IRIDA instances, used in conjunction with auto-irida-azure-upload

  automationmicrobial-genomicsdata-sharing

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 7, 2025Oct 7, 2025

• fluflo

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

  nextflowphylogeneticstrees+ 3nextstrainauspicemicrobes

  Nextflow

  •

  GNU General Public License v3.0

  •4•8•0•0•Updated Oct 2, 2025Oct 2, 2025

• snippy-core-phylogenomics

  Public
  Nextflow

  •2•1•4•1•Updated Oct 2, 2025Oct 2, 2025

• taxon-abundance

  Public
  Python

  •1•5•5•0•Updated Oct 2, 2025Oct 2, 2025

• alignment-variants

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

  microbial-genomicsvariant-callingread-mapping

  Python

  •0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

• cgmlst-clustering

  Public
  Scripts to support clustering of cgMLST allele profiles

  clusteringmicrobial-genomicscgmlst

  C

  •

  MIT License

  •0•3•0•0•Updated Sep 25, 2025Sep 25, 2025

• genomics-qc-site-template

  Public
  Starter template for creating new ClojureScript-based Genomics QC sites

  Clojure

  •0•0•0•0•Updated Sep 24, 2025Sep 24, 2025

• nf-flu

  Public
  Influenza genome analysis Nextflow workflow

  Nextflow

  •

  MIT License

  •24•0•0•0•Updated Sep 15, 2025Sep 15, 2025

• sequencing-runs-collector

  Public
  A service for storing and retrieving info about sequencing runs.

  genomicsnext-generation-sequencing

  Python

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Sep 12, 2025Sep 12, 2025

• auspice-docker

  Public
  Dockerfile

  •0•0•0•0•Updated Sep 11, 2025Sep 11, 2025

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •169•0•0•0•Updated Sep 11, 2025Sep 11, 2025

• tbprofiler-nf

  Public
  Nextflow Wrapper for TBProfiler

  bioinformatics-pipelinemicrobial-genomicstuberculosis-classification

  Python

  •2•4•4•0•Updated Aug 29, 2025Aug 29, 2025

• kma-cgmlst

  Public
  A cgMLST pipeline based on the KMA aligner

  bioinformatics-pipelinemicrobial-genomicscgmlst

  Nextflow

  •

  MIT License

  •2•4•5•0•Updated Aug 28, 2025Aug 28, 2025

• basic-sequence-qc

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

  quality-controlgenomicsnext-generation-sequencing+ 1bioinformatics-pipeline

  Python

  •

  MIT License

  •1•1•0•0•Updated Jul 28, 2025Jul 28, 2025

• its-nf

  Public
  Python

  •0•0•0•0•Updated Jul 21, 2025Jul 21, 2025

• plasmid-screen

  Public
  Screen plasmids for carbapenemase resistance genes, and classify using MOB Suite

  bioinformatics-pipelineantibiotic-resistanceplasmids+ 1genomic-epidemiology

  Python

  •0•2•6•0•Updated Jul 18, 2025Jul 18, 2025

• auto-cpo

  Public
  Automation of Genomic Analyses for Carbapenemase-Producing Organisms (CPOs)

  automationmicrobial-genomics

  Python

  •

  GNU General Public License v3.0

  •0•0•4•0•Updated Jul 18, 2025Jul 18, 2025

• WasteFlow

  Public
  Nextflow pipeline for pathogen surveillance in wastewater

  genomicsnextflowsurveillance+ 4wastewaterfreyjasars-cov-2microbes

  Nextflow

  •

  GNU General Public License v3.0

  •3•7•0•0•Updated Jul 4, 2025Jul 4, 2025

• auto-analysis-template

  Public
  Starter template for creating new nextflow-based analysis automation tools

  project-templatemicrobial-genomicsanalysis-automation

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 4, 2025Jun 4, 2025

• routine-sequence-qc-site

  Public
  A site for displaying routine sequence QC data

  quality-controlclojurescriptnext-generation-sequencing+ 1microbial-genomics

  Clojure

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Jun 3, 2025Jun 3, 2025

• qc-collector-template

  Public
  Starter template for creating new QC Collector tools

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

• mlst-nf

  Public
  Run mlst on multiple samples with integrated quality control.

  microbial-genomicsmlstmicrobial-subtyping

  Nextflow

  •1•1•3•0•Updated May 29, 2025May 29, 2025

• process-nanopore

  Public
  A pipeline for processing raw sequence data from nanopore runs

  Python

  •0•0•0•0•Updated May 16, 2025May 16, 2025

• auto-flu

  Public
  Automated analysis of flu sequence data using BCCDC-PHL/fluviewer-nf

  Python

  •1•1•0•0•Updated May 14, 2025May 14, 2025

• plasmid-surgery

  Public
  Python

  •0•1•0•0•Updated May 8, 2025May 8, 2025