Repositories list

• rsv-a-artic-nf

  Public
  Artic pipeline adapted for RSV-A

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

• rsv-b-artic-nf

  Public
  Artic pipeline workflow adapted for RSV-B

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

• rsv-a-qc

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

• rsv-b-qc

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

• taxon-abundance

  Public
  Python

  •1•5•5•0•Updated Jul 29, 2025Jul 29, 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

  •0•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

• 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 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

• 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 Jul 7, 2025Jul 7, 2025

• WasteFlow

  Public
  Nextflow pipeline for pathogen surveillance in wastewater

  genomicsnextflowsurveillance+ 4wastewaterfreyjasars-cov-2microbes

  Nextflow

  •

  GNU General Public License v3.0

  •3•6•0•0•Updated Jul 4, 2025Jul 4, 2025

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •169•0•0•0•Updated Jun 24, 2025Jun 24, 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

• tbprofiler-nf

  Public
  Nextflow Wrapper for TBProfiler

  bioinformatics-pipelinemicrobial-genomicstuberculosis-classification

  Python

  •2•4•5•0•Updated Jun 2, 2025Jun 2, 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

• auto-hcv

  Public
  Automated genomic analysis of HCV sequence data

  automationmicrobial-genomics

  Python

  •

  MIT License

  •1•0•0•0•Updated Jun 2, 2025Jun 2, 2025

• 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 May 31, 2025May 31, 2025

• mlst-nf

  Public
  Run mlst on multiple samples with integrated quality control.

  microbial-genomicsmlstmicrobial-subtyping

  Nextflow

  •0•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

• alignment-variants

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

  microbial-genomicsvariant-callingread-mapping

  Python

  •0•0•0•0•Updated May 15, 2025May 15, 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

• routine-nanopore-qc

  Public
  Routine sequence QC for nanopore data

  Nextflow

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

• auto-routine-nanopore-qc

  Public
  Python

  •0•0•0•0•Updated May 3, 2025May 3, 2025

• symlink-seqs

  Public
  Create fastq symlinks for selected samples in sequencer output directories based on several criteria

  next-generation-sequencingdata-managementillumina-sequencing+ 1symlinks-manager

  Python

  •0•0•3•0•Updated Apr 29, 2025Apr 29, 2025

• bioinflow

  Public
  Nextflow pipeline for providing public health bioinfo.

  Nextflow

  •

  MIT License

  •0•5•0•0•Updated Apr 27, 2025Apr 27, 2025

• auto-pangolin

  Public
  Automated lineage assignment of SARS-CoV-2 sequences with pangolin

  Python

  •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

• auto-ncov

  Public
  Automated genomic analysis of SARS-CoV-2 sequence data

  automationmicrobial-genomicsgenomic-epidemiology

  Python

  •0•1•3•0•Updated Apr 16, 2025Apr 16, 2025