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@UPHL-BioNGS

UPHL-BioNGS

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  1. Cecret Public

    Reference-based consensus creation

    Nextflow 52 27

  2. Grandeur Public

    UPHL's Reference Free Pipeline

    Nextflow 26 7

  3. walkercreek Public

    A nextflow pipeline that accommodates different sequencing technologies (Illumina or Nanopore), sample types (clinical or wastewater), and viral targets (Influenza or RSV).

    HTML 9 2

  4. Donut_Falls Public

    Basic workflow for nanopore sequencing data

    Nextflow 15 7

Repositories

Showing 10 of 11 repositories
  • Grandeur Public

    UPHL's Reference Free Pipeline

    Nextflow 26 GPL-3.0 7 7 1 Updated Mar 5, 2025
  • Cecret Public

    Reference-based consensus creation

    Nextflow 52 MIT 27 3 0 Updated Mar 4, 2025
  • General_LW_scripts Public

    The scripts that UPHL uses to download things from basespace and run respective workflows

    Python 2 GPL-3.0 2 0 10 Updated Feb 27, 2025
  • walkercreek Public

    A nextflow pipeline that accommodates different sequencing technologies (Illumina or Nanopore), sample types (clinical or wastewater), and viral targets (Influenza or RSV).

    HTML 9 MIT 2 1 0 Updated Feb 24, 2025
  • Dockerfiles Public

    A collection of Dockerfiles for the images that we use

    Dockerfile 0 0 0 0 Updated Feb 19, 2025
  • mycosnp-nf Public Forked from CDCgov/mycosnp-nf

    CDCgov/mycosnp-nf

    Nextflow 0 Apache-2.0 39 0 0 Updated Feb 14, 2025
  • Donut_Falls Public

    Basic workflow for nanopore sequencing data

    Nextflow 15 MIT 7 6 0 Updated Feb 4, 2025
  • Wastewater-genomic-analysis Public
    Python 1 0 1 0 Updated Aug 12, 2024
  • 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 cannot pass config or param files.

    Nextflow 2 GPL-3.0 0 0 0 Updated Sep 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 0 MIT 0 2 0 Updated Aug 26, 2022
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