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@CFIA-NCFAD CFIA NCFAD - Genomics Unit

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    16 repositories

    • nf-flu

      Public
      Influenza genome analysis Nextflow workflow
      Nextflow
      •
      MIT License
      •21•19•10•3•Updated Jan 24, 2025Jan 24, 2025

    • miso_nanopore_runscanner

      Public
      A MISO LIMS Nanopore Run Scanner with pod5 and flowcell re-use support
      Python
      •0•0•1•0•Updated Jan 20, 2025Jan 20, 2025

    • nf-test-datasets

      Public
      Nextflow workflow test datasets for CI
      2•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • 2024-CSV-lab-overview-poster

      Public
      Genomics on the frontline of infectious disease outbreak response and animal health emergency investigations at the Canadian Food Inspection Agency
      Jupyter Notebook
      •0•0•0•0•Updated Sep 18, 2024Sep 18, 2024

    • nim-mqc-versions-yml

      Public
      Nim implementation of Python script to convert a typical Nextflow workflow versions.yml file to a MultiQC custom HTML table
      Nim
      •
      Apache License 2.0
      •0•0•0•0•Updated Aug 7, 2024Aug 7, 2024

    • nf-virontus

      Public
      Oxford Nanopore reference mapping, taxonomic classification, de novo assembly workflow primarily for viral sequence data
      Nextflow
      •3•6•2•0•Updated May 28, 2024May 28, 2024

    • wgscovplot

      Public
      The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth information, variants and DNA Gene features
      JavaScript
      •
      Other
      •5•18•5•1•Updated May 3, 2024May 3, 2024

    • miso-tool

      Public
      Parse the samples and sequencing runs info from MISO Pinery JSON files and generate Nextflow samplesheets and other files
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 26, 2024Apr 26, 2024

    • xlavir

      Public
      HTML
      •
      MIT License
      •2•3•0•0•Updated Dec 6, 2023Dec 6, 2023

    • Delta-SARS-CoV-2-WTD-QC

      Public
      Quebec white-tailed deer SARS-CoV-2 code, Jupyter Notebooks and analysis data and results
      Jupyter Notebook
      •0•0•0•0•Updated Sep 20, 2023Sep 20, 2023

    • gfflu

      Public
      Python CLI app to generate annotations of Influenza A virus (IAV) gene segment nucleotide sequences with BLASTX and Miniprot
      Python
      •
      MIT License
      •0•1•1•0•Updated Aug 9, 2023Aug 9, 2023

    • nf-villumina

      Public
      Generic viral Illumina sequence analysis pipeline
      Nextflow
      •
      MIT License
      •5•5•0•0•Updated Aug 10, 2022Aug 10, 2022

    • .github

      Public
      0•0•0•0•Updated May 6, 2022May 6, 2022

    • scovtree

      Public
      Nextflow
      •
      MIT License
      •2•0•1•0•Updated Dec 19, 2021Dec 19, 2021

    • shiptv

      Public
      Standalone HTML interactive phylogenetic tree visualization powered by Phylocanvas and Javascript
      HTML
      •
      Other
      •3•1•0•0•Updated May 13, 2021May 13, 2021

    • nf-ionampliseq

      Public
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Nov 6, 2020Nov 6, 2020