Repositories list

• irida-next

  Public
  IRIDA Next

  Ruby

  •

  Apache License 2.0

  •3•9•13•7•Updated Jan 7, 2025Jan 7, 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

• gasnomenclature

  Public
  Nomenclature assignment pipeline

  Nextflow

  •

  MIT License

  •0•0•1•1•Updated Jan 6, 2025Jan 6, 2025

• CryptoGenotyper

  Public
  CryptoGenotyper is a tool that allows for subtyping the parasite, Cryptosporidium

  typingpublic-healthcryptosporidium-parasite

  Python

  •1•0•3•0•Updated Jan 3, 2025Jan 3, 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-controlannotation+ 6nextflowassemblypipelinesmetagenomicsbacteriacontamination-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•9•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

• fastmatchirida

  Public
  Quickly refines a reference set of samples based on distance.

  HTML

  •

  MIT License

  •0•1•0•0•Updated Dec 13, 2024Dec 13, 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

  bioinformaticsserotypingsalmonella+ 2cgmlstsistr

  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.

  golangbioinformaticsclustering+ 2parallel-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