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    157 repositories

    • metadatatransformation

      Public
      Nextflow
      •
      MIT License
      •0•0•3•0•Updated Aug 8, 2025Aug 8, 2025

    • mikrokondo

      Public
      A simple pipeline for bacterial assembly and quality control
      bioinformaticsquality-controlannotationnextflowassemblypipelinesmetagenomicsbacteriacontamination-detection
      Nextflow
      •
      MIT License
      •3•17•27•3•Updated Aug 8, 2025Aug 8, 2025

    • irida-next

      Public
      IRIDA Next
      Ruby
      •
      Apache License 2.0
      •3•11•10•18•Updated Aug 8, 2025Aug 8, 2025

    • gasclustering

      Public
      HTML
      •
      MIT License
      •0•0•3•0•Updated Aug 8, 2025Aug 8, 2025

    • fastmatchirida

      Public
      Quickly refines a reference set of samples based on distance.
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Aug 8, 2025Aug 8, 2025

    • snvphylnfc

      Public
      SNVPhyl nf-core Pipeline (Development)
      HTML
      •
      MIT License
      •1•4•5•0•Updated Aug 8, 2025Aug 8, 2025

    • arboratornf

      Public
      EPS suite Arborator pipeline
      HTML
      •
      MIT License
      •0•0•4•0•Updated Aug 8, 2025Aug 8, 2025

    • gasnomenclature

      Public
      Nomenclature assignment pipeline
      Nextflow
      •
      MIT License
      •1•0•4•1•Updated Aug 8, 2025Aug 8, 2025

    • nf-ViralMutations

      Public
      Generic pipeline for calling mutations against a viral reference genome
      Nextflow
      •
      Apache License 2.0
      •1•1•8•0•Updated Aug 7, 2025Aug 7, 2025

    • ArborView

      Public
      A new way to visualize beautiful phylogenetic trees alongside contextual data.
      visualizationphylogenetic-treestreesdendrogramultrametric
      HTML
      •0•2•1•1•Updated Aug 7, 2025Aug 7, 2025

    • legiovue

      Public
      A nextflow pipeline for whole-genome analysis of *Legionella pneumophila*
      Nextflow
      •
      MIT License
      •3•1•8•2•Updated Aug 6, 2025Aug 6, 2025

    • measeq

      Public
      Measles Sequence Analysis and Automation
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Aug 1, 2025Aug 1, 2025

    • arborator

      Public
      Python
      •
      Apache License 2.0
      •1•3•8•3•Updated Jul 31, 2025Jul 31, 2025

    • typingQC

      Public
      Genotyping Quality Control (typingQC)
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

    • iridanextexample2

      Public
      An example pipeline for running on IRIDA-Next with nf-schema
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jul 25, 2025Jul 25, 2025

    • submitdatairidanext

      Public
      Pipeline for submitting data to INSDC databases for IRIDA Next
      next-generation-sequencingfile-transfermicrobial-genomicsdata-sharingdata-submission
      Nextflow
      •
      MIT License
      •0•1•2•0•Updated Jul 18, 2025Jul 18, 2025

    • CryptoGenotyper

      Public
      CryptoGenotyper is a tool that allows for subtyping the parasite, Cryptosporidium
      typingpublic-health18s-rrnacryptosporidium-parasitegp60
      Python
      •1•0•4•0•Updated Jul 16, 2025Jul 16, 2025

    • 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
      •17•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • locidex

      Public
      Common search engine for similarity based typing applications
      Python
      •
      MIT License
      •0•4•14•1•Updated Jul 15, 2025Jul 15, 2025

    • ncov2019-artic-nf

      Public
      A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
      Python
      •
      GNU Affero General Public License v3.0
      •88•2•2•0•Updated Jul 9, 2025Jul 9, 2025

    • wade

      Public
      WGS Analysis and Detection of Molecular Markers (WADE)
      R
      •
      Apache License 2.0
      •3•7•1•0•Updated Jul 3, 2025Jul 3, 2025

    • wade-data

      Public
      Data for WGS Analysis and Detection of Molecular Markers (WADE)
      Apache License 2.0
      •0•1•0•0•Updated Jul 3, 2025Jul 3, 2025

    • genomic-sequencing-test-datasets

      Public
      3•0•0•2•Updated Jun 30, 2025Jun 30, 2025

    • irida-uploader

      Public
      Sequence file uploader for IRIDA
      Python
      •
      Apache License 2.0
      •13•8•12•1•Updated Jun 24, 2025Jun 24, 2025

    • profile_dists

      Public
      Profile Dists: Convenient package for comparing genetic similarity of samples based on allelic profiles
      Python
      •
      Apache License 2.0
      •1•2•8•0•Updated Jun 11, 2025Jun 11, 2025

    • ecoli_serotyping

      Public
      In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping
      Python
      •
      Apache License 2.0
      •12•58•9•2•Updated Jun 5, 2025Jun 5, 2025

    • viralassembly

      Public
      Assemble and QC viral reads with a reference scheme
      Nextflow
      •
      MIT License
      •1•1•0•1•Updated May 23, 2025May 23, 2025

    • irida-plugin-ectyper

      Public
      IRIDA plugin for ECTyper (E.coli in silico typing tool)
      escherichia-coliserotyping
      Java
      •0•2•0•0•Updated May 21, 2025May 21, 2025

    • genomic_address_service

      Public
      Package for clustering sequences de novo and assignment to existing nomenclature
      Python
      •
      Apache License 2.0
      •4•1•15•0•Updated May 21, 2025May 21, 2025

    • PrimerID-nf

      Public
      Rust
      •
      Apache License 2.0
      •0•0•0•0•Updated May 13, 2025May 13, 2025