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    139 repositories

    • ecoli_serotyping

      Public
      In silico prediction of E. coli serotype
      Python
      •
      Apache License 2.0
      •10•48•8•1•Updated Oct 3, 2024Oct 3, 2024

    • irida-next

      Public
      IRIDA Next
      Ruby
      •
      Apache License 2.0
      •3•8•14•13•Updated Oct 3, 2024Oct 3, 2024

    • mikrokondo

      Public
      A simple pipeline for bacterial assembly and quality control
      bioinformaticsquality-controlannotationnextflowassemblypipelinesmetagenomicsbacteriacontamination-detection
      Nextflow
      •
      MIT License
      •2•11•8•1•Updated Oct 3, 2024Oct 3, 2024

    • schedule-pipelines

      Public
      Python
      •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

    • gasnomenclature

      Public
      Nomenclature assignment pipeline
      Nextflow
      •
      MIT License
      •0•0•1•2•Updated Oct 3, 2024Oct 3, 2024

    • sistr_cmd

      Public
      SISTR (Salmonella In Silico Typing Resource) command-line tool
      bioinformaticsserotypingsalmonellacgmlstsistr
      Python
      •
      Apache License 2.0
      •9•24•11•0•Updated Oct 1, 2024Oct 1, 2024

    • arboratornf

      Public
      EPS suite Arborator pipeline
      HTML
      •
      MIT License
      •0•0•3•1•Updated Sep 27, 2024Sep 27, 2024

    • speciesabundance

      Public
      Estimate the relative abundance of sequence reads originating from different species in a sample.
      Nextflow
      •
      MIT License
      •0•5•0•0•Updated Sep 26, 2024Sep 26, 2024

    • genomic_address_service

      Public
      Package for clustering sequences de novo and assignment to existing nomenclature
      Python
      •
      Apache License 2.0
      •2•1•8•1•Updated Sep 24, 2024Sep 24, 2024

    • snvphylnfc

      Public
      SNVPhyl nf-core Pipeline (Development)
      Nextflow
      •
      MIT License
      •1•3•4•0•Updated Sep 23, 2024Sep 23, 2024

    • viralassembly

      Public
      Assemble and QC viral reads with a reference scheme
      Nextflow
      •
      MIT License
      •0•0•0•1•Updated Sep 23, 2024Sep 23, 2024

    • ArborView

      Public
      A way to visualize beautiful phylogenetic trees alongside contextual data.
      HTML
      •0•0•0•1•Updated Sep 20, 2024Sep 20, 2024

    • staramrnf

      Public
      nf-core StarAMR
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Sep 20, 2024Sep 20, 2024

    • gasclustering

      Public
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Sep 10, 2024Sep 10, 2024

    • pangonet

      Public
      Create and manipulate SARS-CoV-2 pango lineages in a phylogenetic network.
      Python
      •
      Apache License 2.0
      •0•1•2•0•Updated Sep 7, 2024Sep 7, 2024

    • wade

      Public
      WGS Analysis and Detection of Molecular Markers (WADE)
      R
      •
      Apache License 2.0
      •2•5•1•0•Updated Sep 6, 2024Sep 6, 2024

    • wade-data

      Public
      Data for WGS Analysis and Detection of Molecular Markers (WADE)
      Apache License 2.0
      •0•1•0•0•Updated Sep 6, 2024Sep 6, 2024

    • iridanextexample

      Public
      An example pipeline for running on IRIDA Next
      nextflowexamplenf-core
      Nextflow
      •
      MIT License
      •3•0•2•0•Updated Sep 3, 2024Sep 3, 2024

    • go-cluster

      Public
      A utility for fast-matching and clustering.
      golangbioinformaticsclusteringparallel-computingphylogenetics
      Go
      •
      Other
      •0•1•0•0•Updated Sep 3, 2024Sep 3, 2024

    • nf-pipelines

      Public
      Creative Commons Attribution 4.0 International
      •0•0•4•0•Updated Aug 27, 2024Aug 27, 2024

    • irida-metadata-uploader

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Aug 23, 2024Aug 23, 2024

    • inext_cli

      Public
      IRIDA Next GraphQL Commandline toolkit
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 21, 2024Aug 21, 2024

    • locidex

      Public
      Common search engine for similarity based typing applications
      Python
      •
      MIT License
      •0•2•13•0•Updated Aug 21, 2024Aug 21, 2024

    • fastmatch-in

      Public
      Fast matching for IRIDANext
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Aug 20, 2024Aug 20, 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•4•0•Updated Aug 20, 2024Aug 20, 2024

    • pipeline-standards

      Public
      Guidelines for developing Nextflow pipelines for IRIDA Next.
      Apache License 2.0
      •1•2•7•0•Updated Aug 13, 2024Aug 13, 2024

    • zebra-browser-print-wrapper

      Public
      JavaScript
      •19•0•0•0•Updated Aug 13, 2024Aug 13, 2024

    • 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
      •0•0•6•1•Updated Jul 31, 2024Jul 31, 2024

    • arborator

      Public
      Python
      •
      Apache License 2.0
      •0•2•4•0•Updated Jul 30, 2024Jul 30, 2024

    • 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
      •89•1•1•0•Updated Jul 24, 2024Jul 24, 2024