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    144 repositories

    • irida-next

      Public
      IRIDA Next
      Ruby
      •
      Apache License 2.0
      •3•9•15•8•Updated Jan 8, 2025Jan 8, 2025

    • fastmatchirida

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

    • gasnomenclature

      Public
      Nomenclature assignment pipeline
      Nextflow
      •
      MIT License
      •0•0•3•0•Updated Jan 8, 2025Jan 8, 2025

    • CryptoGenotyper

      Public
      CryptoGenotyper is a tool that allows for subtyping the parasite, Cryptosporidium
      typingpublic-healthcryptosporidium-parasite
      Python
      •1•0•3•0•Updated Jan 8, 2025Jan 8, 2025

    • irida

      Public
      Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
      Java
      •
      Apache License 2.0
      •31•40•168•4•Updated Jan 7, 2025Jan 7, 2025

    • legiovue

      Public
      A nextflow pipeline for whole-genome analysis of *Legionella pneumophila*
      Nextflow
      •
      MIT License
      •0•0•3•1•Updated Jan 6, 2025Jan 6, 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•10•18•Updated Dec 30, 2024Dec 30, 2024

    • gasclustering

      Public
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Dec 23, 2024Dec 23, 2024

    • mikrokondo

      Public
      A simple pipeline for bacterial assembly and quality control
      bioinformaticsquality-controlannotationnextflowassemblypipelinesmetagenomicsbacteriacontamination-detection
      Nextflow
      •
      MIT License
      •2•15•21•1•Updated Dec 23, 2024Dec 23, 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

    • genomic_address_service

      Public
      Package for clustering sequences de novo and assignment to existing nomenclature
      Python
      •
      Apache License 2.0
      •2•1•10•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•124•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

    • ecoli_serotyping

      Public
      In silico prediction of E. coli serotype
      Python
      •
      Apache License 2.0
      •11•51•7•2•Updated Dec 12, 2024Dec 12, 2024

    • irida-uploader

      Public
      Sequence file uploader for IRIDA
      Python
      •
      Apache License 2.0
      •13•8•12•2•Updated Dec 11, 2024Dec 11, 2024

    • biohansel

      Public
      Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes
      Python
      •
      Apache License 2.0
      •7•26•12•1•Updated Dec 9, 2024Dec 9, 2024

    • sistr_cmd

      Public
      SISTR (Salmonella In Silico Typing Resource) command-line tool
      bioinformaticsserotypingsalmonellacgmlstsistr
      Python
      •
      Apache License 2.0
      •9•26•10•0•Updated Dec 5, 2024Dec 5, 2024

    • viralassembly

      Public
      Assemble and QC viral reads with a reference scheme
      Nextflow
      •
      MIT License
      •1•0•0•1•Updated Nov 29, 2024Nov 29, 2024

    • 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 Nov 26, 2024Nov 26, 2024

    • fetchdatairidanext

      Public
      Pipeline for downloading data from INSDC databases for IRIDA Next.
      Nextflow
      •
      MIT License
      •1•0•2•0•Updated Nov 22, 2024Nov 22, 2024

    • neptune

      Public
      Neptune: Genomic Signature Discovery
      Python
      •
      Apache License 2.0
      •7•19•2•0•Updated Nov 20, 2024Nov 20, 2024

    • ArborView

      Public
      A way to visualize beautiful phylogenetic trees alongside contextual data.
      HTML
      •0•0•1•1•Updated Nov 19, 2024Nov 19, 2024

    • slm

      Public
      Display currently allocated memory across cluster nodes.
      Shell
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • go-cluster

      Public
      A utility for fast-matching and clustering.
      golangbioinformaticsclusteringparallel-computingphylogenetics
      Go
      •
      Other
      •0•1•3•0•Updated Nov 13, 2024Nov 13, 2024

    • arboratornf

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

    • 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