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@CDPHE-bioinformatics

CDPHE GSP Bioinformatics Unit

Colorado Department of Public Health and Environment (CDPHE) - Genomic Surveillance Program (GSP) - Bioinformatic Unit
README.md

CDPHE GSP Bioinformatics

This GitHub organization is for the Bioinformatics Unit of the Genomics Surveillance Program (GSP) within the Colorado Department of Public Health and Environment (CDPHE).

👋 Welcome

GSP leverages the power of next-generation sequencing (NGS) to analyze the genetic makeup of pathogens, providing valuable insights into:

  • Disease outbreaks: Identifying the source and spread of outbreaks, enabling rapid response and containment.
  • Sentinel surveillance: Capturing the genetic changes that drive pathogen evolution to inform vaccine development and other preventative measures.
  • Wastewater surveillance: Measuring community-level disease prevalence, enabling early detection and intervention.

📑 Contents

Here we share our pipelines and various assets used to monitor infectious diseases.

🎁 Contributing

We welcome contributions from the scientific community to enhance the program's capabilities and impact. Please refer to our Wiki or individual repository guidelines for more information about contributing.

⚠️ Disclaimer

The contents of this organization are intended for research and public health purposes only. The information provided should not be used for clinical decision-making.

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  1. CDPHE-SARS-CoV-2 CDPHE-SARS-CoV-2 Public

    Workflows and scripts for the assembly and analysis of SARS-CoV-2 whole genome tiled amplicon sequencing.

    Python 5 1

  2. CDPHE-influenza CDPHE-influenza Public

    Workflows and scripts for the assembly and analysis of influenza whole genome amplicon sequencing.

    WDL 3 1

  3. CDPHE-RSV CDPHE-RSV Public

    Workflows and scripts for the assembly and analysis of RSV whole genome tiled amplicon sequencing.

    WDL 1

  4. CDPHE-H5-influenza CDPHE-H5-influenza Public

    Workflows and scripts for the assembly and analysis of H5 influenza

    Jupyter Notebook

  5. CDPHE-Enterovirus CDPHE-Enterovirus Public

    Workflows and scripts for the assembly and analysis of enterovirus whole genome sequencing.

    WDL 1

Repositories

Showing 10 of 17 repositories
  • CDPHE-analysis-tools Public

    Useful workflows and tasks for CDPHE pipelines.

    CDPHE-bioinformatics/CDPHE-analysis-tools's past year of commit activity
    WDL 1 0 1 0 Updated Aug 14, 2026
  • cdphe-influenza-wastewater-analysis Public

    WDL workflows for 1) Freyja analysis and 2) alignment of clinical samples amplified with universal primers to Freyja references

    CDPHE-bioinformatics/cdphe-influenza-wastewater-analysis's past year of commit activity
    WDL 0 GPL-3.0 0 0 0 Updated Aug 7, 2026
  • CDPHE-H5-influenza Public

    Workflows and scripts for the assembly and analysis of H5 influenza

    CDPHE-bioinformatics/CDPHE-H5-influenza's past year of commit activity
    Jupyter Notebook 0 GPL-3.0 0 4 1 Updated Aug 3, 2026
  • amplicon-nf Public Forked from sam-baird/amplicon-nf

    Amplicon genome assembly for ARTIC style primer schemes using Nextflow.

    CDPHE-bioinformatics/amplicon-nf's past year of commit activity
    Nextflow 0 MIT 7 0 1 Updated Jul 22, 2026
  • google-batch-cleanup Public

    Cancel any Google Batch child jobs associated with an aborted Seqera Platform workflow

    CDPHE-bioinformatics/google-batch-cleanup's past year of commit activity
    Shell 0 GPL-3.0 0 0 0 Updated Jul 22, 2026
  • AMRplusplus Public Forked from Microbial-Ecology-Group/AMRplusplus

    AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.

    CDPHE-bioinformatics/AMRplusplus's past year of commit activity
    Nextflow 0 GPL-3.0 19 0 0 Updated Jun 23, 2026
  • CDPHE-Enterovirus Public

    Workflows and scripts for the assembly and analysis of enterovirus whole genome sequencing.

    CDPHE-bioinformatics/CDPHE-Enterovirus's past year of commit activity
    WDL 1 GPL-3.0 0 0 0 Updated Apr 1, 2026
  • .github Public

    Repository for our GitHub Organization.

    CDPHE-bioinformatics/.github's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Mar 25, 2026
  • CDPHE-SARS-CoV-2 Public

    Workflows and scripts for the assembly and analysis of SARS-CoV-2 whole genome tiled amplicon sequencing.

    CDPHE-bioinformatics/CDPHE-SARS-CoV-2's past year of commit activity
    Python 5 GPL-3.0 1 11 0 Updated Feb 19, 2026
  • ncbi-cluster-tracker Public

    Create standalone HTML reports for tracking SNP clusters within NCBI Pathogen Detection

    CDPHE-bioinformatics/ncbi-cluster-tracker's past year of commit activity
    Python 5 GPL-3.0 1 2 0 Updated Feb 10, 2026
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