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@UPHL-BioNGS UPHL-BioNGS

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    12 repositories

    • General_LW_scripts

      Public
      The scripts that UPHL uses to download things from basespace and run respective workflows
      bioinformatics
      bioinformatics
      Python
      •
      GNU General Public License v3.0
      •4•2•0•2•Updated Oct 14, 2026Oct 14, 2026

    • Cecret

      Public
      Reference-based consensus creation
      bioinformaticsnextflowphylogenetics
      bioinformaticsnextflowphylogeneticspublic-healthvariant-callingampliconviral-genomicswastewatermafftivar
      Nextflow
      •
      MIT License
      •31•61•6•0•Updated Oct 13, 2026Oct 13, 2026

    • Donut_Falls

      Public
      Assembly of Nanopore Sequencing
      bioinformaticsnanoporenextflow
      bioinformaticsnanoporenextflowdenovo-assemblybandagepolishinghybrid-assemblyfastpbuscounicycler
      Nextflow
      •
      MIT License
      •7•17•3•0•Updated Oct 9, 2026Oct 9, 2026

    • Grandeur

      Public
      UPHL's Reference Free Pipeline
      dockerbioinformaticsgenomics
      dockerbioinformaticsgenomicsnextflowngsphylogeneticsilluminadenovo-assemblyserotypingsalmonella
      Nextflow
      •
      GNU General Public License v3.0
      •7•29•2•0•Updated Oct 9, 2026Oct 9, 2026

    • Wastewater-genomic-analysis

      Public
      Shell
      •0•1•1•0•Updated Jul 8, 2026Jul 8, 2026

    • walkercreek

      Public
      A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.
      bioinformaticspipelinegenomics
      bioinformaticspipelinegenomicsnextflowpublic-healthirmavariant-callinginfluenzailluminaoxford-nanopore
      Nextflow
      •
      MIT License
      •3•10•0•0•Updated Jun 9, 2026Jun 9, 2026

    • Dockerfiles

      Public
      A collection of Dockerfiles for the images that we use
      Dockerfile
      •0•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • neissflow

      Public
      Nextflow pipeline for Neisseria gonorrhoeae isolate analysis
      Nextflow
      •
      Apache License 2.0
      •3•0•0•0•Updated May 14, 2025May 14, 2025

    • mycosnp-nf

      Public
      CDCgov/mycosnp-nf
      Nextflow
      •
      Apache License 2.0
      •45•0•0•0•Updated Feb 14, 2025Feb 14, 2025

    • ICA_Modified_Nextflow_Scripts

      Public
      To be able to run Nextflow scripts that are published on Github on ICA they must be modified because ICA does not have Nextflow do a gitpull and an ICA user can…
      nextflowica
      nextflowica
      Nextflow
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Sep 6, 2023Sep 6, 2023

    • Nextstrain_Build

      Public
      A Nextflow Script that performs a Nextstrain 'Build' which creates a detailed phylogentic visualization that can be seen with the Nextstain Auspice tool.
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Aug 26, 2022Aug 26, 2022

    • UPHL

      Public archive
      The fun things we use and share at UPHL
      Shell
      •
      MIT License
      •1•5•0•0•Updated Mar 11, 2021Mar 11, 2021
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