Repositories list

• irida-next

  Public
  IRIDA Next

  Ruby

  •

  Apache License 2.0

  •55 forks in phac-nml/irida-next•1515 stars in phac-nml/irida-next•1515 issues in phac-nml/irida-next•2222 pull requests in phac-nml/irida-next•Updated Oct 30, 2026Oct 30, 2026

• arboratornf

  Public
  EPS suite Arborator pipeline

  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •00 forks in phac-nml/arboratornf•00 stars in phac-nml/arboratornf•88 issues in phac-nml/arboratornf•11 pull request in phac-nml/arboratornf•Updated Oct 29, 2026Oct 29, 2026

• vira

  Public
  Assemble and QC viral reads with a reference scheme

  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •11 fork in phac-nml/vira•33 stars in phac-nml/vira•00 issues in phac-nml/vira•11 pull request in phac-nml/vira•Updated Oct 29, 2026Oct 29, 2026

• pathogen-view-components

  Public
  Rails ViewComponent gem providing accessible, i18n-ready UI components with Stimulus controllers, built by the Public Health Agency of Canada's Bioinformatics t…

  JavaScript

  •

  Apache License 2.0

  •00 forks in phac-nml/pathogen-view-components•00 stars in phac-nml/pathogen-view-components•1010 issues in phac-nml/pathogen-view-components•1616 pull requests in phac-nml/pathogen-view-components•Updated Oct 28, 2026Oct 28, 2026

• speciesabundance

  Public
  Estimate the relative abundance of sequence reads originating from different species in a sample.

  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •11 fork in phac-nml/speciesabundance•88 stars in phac-nml/speciesabundance•00 issues in phac-nml/speciesabundance•22 pull requests in phac-nml/speciesabundance•Updated Oct 23, 2026Oct 23, 2026

• mikrokondo

  Public
  A simple pipeline for bacterial assembly and quality control

  bioinformaticsquality-controlannotation+ 8

  bioinformaticsquality-controlannotationnextflowassemblypipelinesmetagenomicsbacteriacontamination-detectiongsp-pipeline+ 1

  Nextflow

  •

  MIT License

  •55 forks in phac-nml/mikrokondo•1717 stars in phac-nml/mikrokondo•2121 issues in phac-nml/mikrokondo•33 pull requests in phac-nml/mikrokondo•Updated Oct 22, 2026Oct 22, 2026

• typingQC

  Public
  Genotyping Quality Control (typingQC)

  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •00 forks in phac-nml/typingQC•11 star in phac-nml/typingQC•00 issues in phac-nml/typingQC•00 pull requests in phac-nml/typingQC•Updated Oct 21, 2026Oct 21, 2026

• beave

  Public
  A very Canadian utility for genomic clustering and distance querying.

  bioinformaticsgenomicsclustering

  bioinformaticsgenomicsclustering

  Python

  •00 forks in phac-nml/beave•11 star in phac-nml/beave•77 issues in phac-nml/beave•00 pull requests in phac-nml/beave•Updated Oct 19, 2026Oct 19, 2026

• measeq

  Public
  Measles Sequence Analysis and Automation

  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •77 forks in phac-nml/measeq•1212 stars in phac-nml/measeq•00 issues in phac-nml/measeq•11 pull request in phac-nml/measeq•Updated Oct 16, 2026Oct 16, 2026

• azure-blob

  Public
  Azure blob client and Active Storage adapter.

  Ruby

  •

  MIT License

  •1818 forks in phac-nml/azure-blob•00 stars in phac-nml/azure-blob•00 issues in phac-nml/azure-blob•00 pull requests in phac-nml/azure-blob•Updated Oct 15, 2026Oct 15, 2026

• iridanextexample2

  Public
  An example pipeline for running on IRIDA-Next with nf-schema

  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •00 forks in phac-nml/iridanextexample2•00 stars in phac-nml/iridanextexample2•00 issues in phac-nml/iridanextexample2•11 pull request in phac-nml/iridanextexample2•Updated Oct 8, 2026Oct 8, 2026

• gasnomenclature

  Public
  Nomenclature assignment pipeline

  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •11 fork in phac-nml/gasnomenclature•00 stars in phac-nml/gasnomenclature•44 issues in phac-nml/gasnomenclature•00 pull requests in phac-nml/gasnomenclature•Updated Oct 7, 2026Oct 7, 2026

• gasclustering

  Public
  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  HTML

  •

  MIT License

  •00 forks in phac-nml/gasclustering•00 stars in phac-nml/gasclustering•33 issues in phac-nml/gasclustering•00 pull requests in phac-nml/gasclustering•Updated Oct 7, 2026Oct 7, 2026

• legiovue

  Public
  A nextflow pipeline for whole-genome analysis of *Legionella pneumophila*

  Nextflow

  •

  MIT License

  •55 forks in phac-nml/legiovue•44 stars in phac-nml/legiovue•44 issues in phac-nml/legiovue•22 pull requests in phac-nml/legiovue•Updated Oct 5, 2026Oct 5, 2026

• snvphylnfc

  Public
  SNVPhyl nf-core Pipeline (Development)

  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  HTML

  •

  MIT License

  •11 fork in phac-nml/snvphylnfc•88 stars in phac-nml/snvphylnfc•77 issues in phac-nml/snvphylnfc•00 pull requests in phac-nml/snvphylnfc•Updated Oct 2, 2026Oct 2, 2026

• specid-nf

  Public
  Nextflow

  •

  MIT License

  •00 forks in phac-nml/specid-nf•00 stars in phac-nml/specid-nf•00 issues in phac-nml/specid-nf•00 pull requests in phac-nml/specid-nf•Updated Sep 17, 2026Sep 17, 2026

• metadatatransformation

  Public
  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •00 forks in phac-nml/metadatatransformation•00 stars in phac-nml/metadatatransformation•33 issues in phac-nml/metadatatransformation•11 pull request in phac-nml/metadatatransformation•Updated Sep 16, 2026Sep 16, 2026

• staramrnf

  Public
  nf-core StarAMR

  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •11 fork in phac-nml/staramrnf•11 star in phac-nml/staramrnf•22 issues in phac-nml/staramrnf•00 pull requests in phac-nml/staramrnf•Updated Sep 14, 2026Sep 14, 2026

• sapporo-service

  Public
  A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification.

  HTML

  •

  Apache License 2.0

  •1515 forks in phac-nml/sapporo-service•00 stars in phac-nml/sapporo-service•00 issues in phac-nml/sapporo-service•00 pull requests in phac-nml/sapporo-service•Updated Sep 8, 2026Sep 8, 2026

• submitdatairidanext

  Public
  Pipeline for submitting data to INSDC databases for IRIDA Next

  next-generation-sequencingfile-transfermicrobial-genomics+ 4

  next-generation-sequencingfile-transfermicrobial-genomicsdata-sharingdata-submissiongsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •00 forks in phac-nml/submitdatairidanext•11 star in phac-nml/submitdatairidanext•22 issues in phac-nml/submitdatairidanext•11 pull request in phac-nml/submitdatairidanext•Updated Aug 26, 2026Aug 26, 2026

• fastmatchirida

  Public
  Quickly refines a reference set of samples based on distance.

  gsp-pipelineiridanext-pipeline

  gsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •00 forks in phac-nml/fastmatchirida•11 star in phac-nml/fastmatchirida•11 issue in phac-nml/fastmatchirida•00 pull requests in phac-nml/fastmatchirida•Updated Aug 18, 2026Aug 18, 2026

• wade

  Public
  WGS Analysis and Detection of Molecular Markers (WADE)

  R

  •

  Apache License 2.0

  •44 forks in phac-nml/wade•1010 stars in phac-nml/wade•11 issue in phac-nml/wade•00 pull requests in phac-nml/wade•Updated Aug 6, 2026Aug 6, 2026

• wade-data

  Public
  Data for WGS Analysis and Detection of Molecular Markers (WADE)

  Apache License 2.0

  •00 forks in phac-nml/wade-data•11 star in phac-nml/wade-data•00 issues in phac-nml/wade-data•00 pull requests in phac-nml/wade-data•Updated Aug 6, 2026Aug 6, 2026

• puppet-irida

  Public
  The IRIDA module lets you use Puppet to install, deploy, and configure IRIDA web server (Alpha status)

  Puppet

  •

  Apache License 2.0

  •00 forks in phac-nml/puppet-irida•00 stars in phac-nml/puppet-irida•66 issues in phac-nml/puppet-irida•00 pull requests in phac-nml/puppet-irida•Updated Jul 20, 2026Jul 20, 2026

• irida-uploader

  Public
  Sequence file uploader for IRIDA

  Python

  •

  Apache License 2.0

  •1414 forks in phac-nml/irida-uploader•88 stars in phac-nml/irida-uploader•1212 issues in phac-nml/irida-uploader•11 pull request in phac-nml/irida-uploader•Updated Jul 16, 2026Jul 16, 2026

• ArborView

  Public
  A new way to visualize beautiful phylogenetic trees alongside contextual data.

  visualizationphylogenetic-treestrees+ 2

  visualizationphylogenetic-treestreesdendrogramultrametric

  HTML

  •11 fork in phac-nml/ArborView•44 stars in phac-nml/ArborView•11 issue in phac-nml/ArborView•22 pull requests in phac-nml/ArborView•Updated Jun 29, 2026Jun 29, 2026

• galaxy_tools

  Public
  Contains a set of Galaxy Tools mostly written by the Bioinformatics core at NML

  Perl

  •

  Apache License 2.0

  •2626 forks in phac-nml/galaxy_tools•1515 stars in phac-nml/galaxy_tools•1111 issues in phac-nml/galaxy_tools•1616 pull requests in phac-nml/galaxy_tools•Updated Jun 12, 2026Jun 12, 2026

• staramr

  Public
  Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

  bioinformaticsgenomicsantimicrobial-resistance

  bioinformaticsgenomicsantimicrobial-resistance

  Python

  •

  Apache License 2.0

  •3030 forks in phac-nml/staramr•209209 stars in phac-nml/staramr•1818 issues in phac-nml/staramr•00 pull requests in phac-nml/staramr•Updated Jun 10, 2026Jun 10, 2026

• nf-iridanext

  Public
  Plugin for integration of Nextflow pipelines with IRIDA Next.

  Groovy

  •

  Apache License 2.0

  •00 forks in phac-nml/nf-iridanext•66 stars in phac-nml/nf-iridanext•88 issues in phac-nml/nf-iridanext•00 pull requests in phac-nml/nf-iridanext•Updated Jun 4, 2026Jun 4, 2026

• iridanextexample

  Public
  An example pipeline for running on IRIDA Next

  nextflowexamplenf-core+ 2

  nextflowexamplenf-coregsp-pipelineiridanext-pipeline

  Nextflow

  •

  MIT License

  •33 forks in phac-nml/iridanextexample•11 star in phac-nml/iridanextexample•22 issues in phac-nml/iridanextexample•11 pull request in phac-nml/iridanextexample•Updated Jun 1, 2026Jun 1, 2026