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    • IRIDA Next
      Ruby
      Apache License 2.0
      39148Updated Dec 22, 2024Dec 22, 2024
    • Profile Dists: Convenient package for comparing genetic similarity of samples based on allelic profiles
      Python
      Apache License 2.0
      1260Updated Dec 20, 2024Dec 20, 2024
    • CryptoGenotyper is a tool that allows for subtyping the parasite, Cryptosporidium
      Python
      1030Updated Dec 20, 2024Dec 20, 2024
    • Contains a set of Galaxy Tools mostly written by the Bioinformatics core at NML
      Perl
      Apache License 2.0
      25151019Updated Dec 20, 2024Dec 20, 2024
    • Package for clustering sequences de novo and assignment to existing nomenclature
      Python
      Apache License 2.0
      2190Updated Dec 20, 2024Dec 20, 2024
    • irida

      Public
      Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
      Java
      Apache License 2.0
      31401683Updated Dec 20, 2024Dec 20, 2024
    • legiovue

      Public
      A nextflow pipeline for whole-genome analysis of *Legionella pneumophila*
      Nextflow
      MIT License
      0030Updated Dec 19, 2024Dec 19, 2024
    • Creative Commons Attribution 4.0 International
      0040Updated Dec 19, 2024Dec 19, 2024
    • 2001Updated Dec 18, 2024Dec 18, 2024
    • staramr

      Public
      Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
      Python
      Apache License 2.0
      28119170Updated Dec 16, 2024Dec 16, 2024
    • Quickly refines a reference set of samples based on distance.
      HTML
      MIT License
      0100Updated Dec 13, 2024Dec 13, 2024
    • A set of tools designed for ONT sequencing analysis, enabling the exploration and comparison of sequencing outcomes across experimental conditions.
      Python
      Other
      1500Updated Dec 12, 2024Dec 12, 2024
    • In silico prediction of E. coli serotype
      Python
      Apache License 2.0
      125062Updated Dec 12, 2024Dec 12, 2024
    • Sequence file uploader for IRIDA
      Python
      Apache License 2.0
      138122Updated Dec 11, 2024Dec 11, 2024
    • biohansel

      Public
      Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes
      Python
      Apache License 2.0
      726121Updated Dec 9, 2024Dec 9, 2024
    • sistr_cmd

      Public
      SISTR (Salmonella In Silico Typing Resource) command-line tool
      Python
      Apache License 2.0
      92590Updated Dec 5, 2024Dec 5, 2024
    • Assemble and QC viral reads with a reference scheme
      Nextflow
      MIT License
      1001Updated Nov 29, 2024Nov 29, 2024
    • A simple pipeline for bacterial assembly and quality control
      Nextflow
      MIT License
      215200Updated Nov 27, 2024Nov 27, 2024
    • A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification.
      HTML
      Apache License 2.0
      17000Updated Nov 26, 2024Nov 26, 2024
    • Pipeline for downloading data from INSDC databases for IRIDA Next.
      Nextflow
      MIT License
      1020Updated Nov 22, 2024Nov 22, 2024
    • neptune

      Public
      Neptune: Genomic Signature Discovery
      Python
      Apache License 2.0
      71920Updated Nov 20, 2024Nov 20, 2024
    • ArborView

      Public
      A way to visualize beautiful phylogenetic trees alongside contextual data.
      HTML
      0011Updated Nov 19, 2024Nov 19, 2024
    • slm

      Public
      Display currently allocated memory across cluster nodes.
      Shell
      Apache License 2.0
      0000Updated Nov 15, 2024Nov 15, 2024
    • A utility for fast-matching and clustering.
      Go
      Other
      0130Updated Nov 13, 2024Nov 13, 2024
    • Nextflow
      MIT License
      0020Updated Nov 7, 2024Nov 7, 2024
    • EPS suite Arborator pipeline
      Nextflow
      MIT License
      0030Updated Nov 5, 2024Nov 5, 2024
    • A tool for importing data from IRIDA into Galaxy
      Python
      Apache License 2.0
      3731Updated 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
      0100Updated Nov 1, 2024Nov 1, 2024
    • Nomenclature assignment pipeline
      Nextflow
      MIT License
      0001Updated Nov 1, 2024Nov 1, 2024
    • wade

      Public
      WGS Analysis and Detection of Molecular Markers (WADE)
      R
      Apache License 2.0
      3510Updated Oct 23, 2024Oct 23, 2024