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    146 repositories

    • mikrokondo

      Public
      A simple pipeline for bacterial assembly and quality control
      bioinformaticsquality-controlannotationnextflowassemblypipelinesmetagenomicsbacteriacontamination-detection
      Nextflow
      •
      MIT License
      •2•15•22•3•Updated Feb 7, 2025Feb 7, 2025

    • irida-next

      Public
      IRIDA Next
      Ruby
      •
      Apache License 2.0
      •3•9•15•8•Updated Feb 7, 2025Feb 7, 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•1•Updated Feb 7, 2025Feb 7, 2025

    • locidex

      Public
      Common search engine for similarity based typing applications
      Python
      •
      MIT License
      •0•4•13•0•Updated Feb 7, 2025Feb 7, 2025

    • viralassembly

      Public
      Assemble and QC viral reads with a reference scheme
      Nextflow
      •
      MIT License
      •1•0•0•1•Updated Feb 7, 2025Feb 7, 2025

    • metadatatransformation

      Public
      Nextflow
      •
      MIT License
      •0•0•0•1•Updated Feb 7, 2025Feb 7, 2025

    • azure-blob

      Public
      Azure blob client and Active Storage adapter.
      Ruby
      •
      MIT License
      •5•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • irida

      Public
      Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
      Java
      •
      Apache License 2.0
      •31•40•169•8•Updated Feb 6, 2025Feb 6, 2025

    • gasnomenclature

      Public
      Nomenclature assignment pipeline
      Nextflow
      •
      MIT License
      •1•0•5•2•Updated Feb 6, 2025Feb 6, 2025

    • gasclustering

      Public
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Feb 4, 2025Feb 4, 2025

    • arboratornf

      Public
      EPS suite Arborator pipeline
      Nextflow
      •
      MIT License
      •0•0•3•0•Updated Feb 4, 2025Feb 4, 2025

    • nf-iridanext

      Public
      Plugin for integration of Nextflow pipelines with IRIDA Next.
      Groovy
      •
      Apache License 2.0
      •0•5•5•1•Updated Feb 4, 2025Feb 4, 2025

    • wade

      Public
      WGS Analysis and Detection of Molecular Markers (WADE)
      R
      •
      Apache License 2.0
      •3•5•1•0•Updated Feb 3, 2025Feb 3, 2025

    • CryptoGenotyper

      Public
      CryptoGenotyper is a tool that allows for subtyping the parasite, Cryptosporidium
      typingpublic-healthcryptosporidium-parasite
      Python
      •1•0•4•0•Updated Jan 31, 2025Jan 31, 2025

    • legiovue

      Public
      A nextflow pipeline for whole-genome analysis of *Legionella pneumophila*
      Nextflow
      •
      MIT License
      •2•1•4•0•Updated Jan 31, 2025Jan 31, 2025

    • pipeline-standards

      Public
      Guidelines for developing Nextflow pipelines for IRIDA Next.
      Apache License 2.0
      •1•2•7•0•Updated Jan 31, 2025Jan 31, 2025

    • genomic_address_service

      Public
      Package for clustering sequences de novo and assignment to existing nomenclature
      Python
      •
      Apache License 2.0
      •3•1•8•0•Updated Jan 31, 2025Jan 31, 2025

    • irida-plugin-ectyper

      Public
      IRIDA plugin for ECTyper (E.coli in silico typing tool)
      escherichia-coliserotyping
      Java
      •0•2•0•0•Updated Jan 30, 2025Jan 30, 2025

    • ecoli_serotyping

      Public
      In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping
      Python
      •
      Apache License 2.0
      •11•51•6•2•Updated Jan 22, 2025Jan 22, 2025

    • wade-data

      Public
      Data for WGS Analysis and Detection of Molecular Markers (WADE)
      Apache License 2.0
      •0•1•0•0•Updated Jan 17, 2025Jan 17, 2025

    • fastmatchirida

      Public
      Quickly refines a reference set of samples based on distance.
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Jan 17, 2025Jan 17, 2025

    • schedule-pipelines

      Public
      Python
      •0•0•1•0•Updated Jan 17, 2025Jan 17, 2025

    • irida-plugin-sistr

      Public
      IRIDA Plugin for SISTR Salmonella Typing Tool
      Java
      •0•0•2•0•Updated Jan 17, 2025Jan 17, 2025

    • galaxy_tools

      Public
      Contains a set of Galaxy Tools mostly written by the Bioinformatics core at NML
      Perl
      •
      Apache License 2.0
      •25•15•11•18•Updated Dec 30, 2024Dec 30, 2024

    • irida-galaxy-importer

      Public
      A tool for importing data from IRIDA into Galaxy
      Python
      •
      Apache License 2.0
      •3•7•3•0•Updated Dec 23, 2024Dec 23, 2024

    • profile_dists

      Public
      Profile Dists: Convenient package for comparing genetic similarity of samples based on allelic profiles
      Python
      •
      Apache License 2.0
      •1•2•6•0•Updated Dec 20, 2024Dec 20, 2024

    • nf-pipelines

      Public
      Creative Commons Attribution 4.0 International
      •0•0•4•0•Updated Dec 19, 2024Dec 19, 2024

    • genomic-sequencing-test-datasets

      Public
      2•0•0•1•Updated Dec 18, 2024Dec 18, 2024

    • staramr

      Public
      Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
      bioinformaticsgenomicsantimicrobial-resistance
      Python
      •
      Apache License 2.0
      •28•130•17•0•Updated Dec 16, 2024Dec 16, 2024

    • sequenoscope

      Public
      A set of tools designed for ONT sequencing analysis, enabling the exploration and comparison of sequencing outcomes across experimental conditions.
      Python
      •
      Other
      •1•5•0•0•Updated Dec 12, 2024Dec 12, 2024