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    141 repositories

    • mikrokondo

      Public
      A simple pipeline for bacterial assembly and quality control
      bioinformaticsquality-controlannotationnextflowassemblypipelinesmetagenomicsbacteriacontamination-detection
      Nextflow
      •
      MIT License
      •2•15•20•1•Updated Nov 5, 2024Nov 5, 2024

    • neptune

      Public
      Neptune: Genomic Signature Discovery
      Python
      •
      Apache License 2.0
      •7•18•2•0•Updated Nov 5, 2024Nov 5, 2024

    • irida-next

      Public
      IRIDA Next
      Ruby
      •
      Apache License 2.0
      •3•8•11•5•Updated Nov 5, 2024Nov 5, 2024

    • irida

      Public
      Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
      Java
      •
      Apache License 2.0
      •31•40•166•15•Updated Nov 5, 2024Nov 5, 2024

    • gasclustering

      Public
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Nov 5, 2024Nov 5, 2024

    • arboratornf

      Public
      EPS suite Arborator pipeline
      Nextflow
      •
      MIT License
      •0•0•3•0•Updated Nov 5, 2024Nov 5, 2024

    • irida-galaxy-importer

      Public
      A tool for importing data from IRIDA into Galaxy
      Python
      •
      Apache License 2.0
      •3•7•3•1•Updated Nov 4, 2024Nov 4, 2024

    • covtrim

      Public
      CovTrim is a specialized bioinformatics tool designed for precise coverage-based downsampling of FASTQ files from amplicon sequencing data.
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Nov 1, 2024Nov 1, 2024

    • gasnomenclature

      Public
      Nomenclature assignment pipeline
      Nextflow
      •
      MIT License
      •0•0•0•1•Updated Nov 1, 2024Nov 1, 2024

    • fetchdatairidanext

      Public
      Pipeline for downloading data from INSDC databases for IRIDA Next.
      Nextflow
      •
      MIT License
      •1•0•2•0•Updated Oct 29, 2024Oct 29, 2024

    • ecoli_serotyping

      Public
      In silico prediction of E. coli serotype
      Python
      •
      Apache License 2.0
      •11•49•6•1•Updated Oct 28, 2024Oct 28, 2024

    • wade

      Public
      WGS Analysis and Detection of Molecular Markers (WADE)
      R
      •
      Apache License 2.0
      •3•5•1•0•Updated Oct 23, 2024Oct 23, 2024

    • wade-data

      Public
      Data for WGS Analysis and Detection of Molecular Markers (WADE)
      Apache License 2.0
      •0•1•0•0•Updated Oct 23, 2024Oct 23, 2024

    • snvphylnfc

      Public
      SNVPhyl nf-core Pipeline (Development)
      Nextflow
      •
      MIT License
      •1•3•5•0•Updated Oct 21, 2024Oct 21, 2024

    • genomic-sequencing-test-datasets

      Public
      0•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • iridanextexample

      Public
      An example pipeline for running on IRIDA Next
      nextflowexamplenf-core
      Nextflow
      •
      MIT License
      •3•0•2•0•Updated Oct 18, 2024Oct 18, 2024

    • ArborView

      Public
      A way to visualize beautiful phylogenetic trees alongside contextual data.
      HTML
      •0•0•1•2•Updated Oct 10, 2024Oct 10, 2024

    • viralassembly

      Public
      Assemble and QC viral reads with a reference scheme
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • mob-suite

      Public
      MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
      clusteringtypingassembliesplasmidshost-range
      Python
      •
      Apache License 2.0
      •33•121•15•1•Updated Oct 9, 2024Oct 9, 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•0•Updated Oct 7, 2024Oct 7, 2024

    • schedule-pipelines

      Public
      Python
      •0•0•0•0•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•25•11•0•Updated Oct 1, 2024Oct 1, 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•10•1•Updated Sep 24, 2024Sep 24, 2024

    • staramrnf

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

    • 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